From 1218956816f2a97ce3cf7b8f889f77f1e85bdde3 Mon Sep 17 00:00:00 2001
From: cwhelan <cwhelan@broadinstitute.org>
Date: Thu, 29 Oct 2020 09:31:43 -0400
Subject: [PATCH] Fix to quality score calculation for sites with spanning
 deletions (#6859)

* fix off-by one error that was causing the qual calculation to miss probability assigned to homozygous star allele genotypes
* make sure we output all sites if forceOutput it true, even if low-qual
* updates to handle the case where the only alleles are ref and star
* add update expected results option to GenotypeGVCFsIntegrationTest
* update integration test files
---
 .../tools/walkers/GenotypeGVCFs.java          |    2 +-
 .../tools/walkers/GenotypeGVCFsEngine.java    |    1 +
 .../afcalc/AlleleFrequencyCalculator.java     |    6 +-
 .../walkers/GenotypeGVCFsIntegrationTest.java |   31 +-
 ...ombined.gatk3.7_30_ga4f720357.expected.vcf |    4 +-
 ....7_30_ga4f720357.24_sample.21.expected.vcf |    4 +-
 ...ed.testGVCFMode.gatk4.alleleSpecific.g.vcf |    2 +-
 ...estGVCFMode.gatk4.alleleSpecific.g.vcf.idx |  Bin 40809 -> 40808 bytes
 .../expected.testGVCFMode.gatk4.g.vcf         |    2 +-
 .../expected.testGVCFMode.gatk4.g.vcf.idx     |  Bin 40794 -> 40793 bytes
 .../expected.testLinkedDebruijnMode.gatk4.vcf |    2 +-
 ...ected.testLinkedDebruijnMode.gatk4.vcf.idx |  Bin 2928 -> 2927 bytes
 .../expected.testVCFMode.gatk4.nonstrict.vcf  |    2 +-
 .../expected.testVCFMode.gatk4.vcf            |    2 +-
 .../walkers/CombineGVCFs/IntervalTest.vcf.idx |  Bin 2147 -> 2152 bytes
 .../convertToBasePairResolution.vcf.idx       |  Bin 2429 -> 2434 bytes
 .../CombineGVCFs/newMQcalc.combined.g.vcf.idx |  Bin 42521 -> 42526 bytes
 ...ingDeletionRestrictToStartExpected.vcf.idx |  Bin 373 -> 378 bytes
 .../testAlleleSpecificAnnotations.vcf.idx     |  Bin 44873 -> 44878 bytes
 ...stAlleleSpecificAnnotationsNoGroup.vcf.idx |  Bin 44880 -> 44885 bytes
 .../testBasepairResolutionInput.vcf.idx       |  Bin 42147 -> 42152 bytes
 .../testBreakBandsArgumet.vcf.idx             |  Bin 2161 -> 2166 bytes
 ...tipleSpanningDeletionsForOneSample.vcf.idx |  Bin 432 -> 437 bytes
 ...anningDeletionsForOneSampleHaploid.vcf.idx |  Bin 439 -> 444 bytes
 ...ingDeletionsForOneSampleTetraploid.vcf.idx |  Bin 442 -> 447 bytes
 .../testWrongReferenceBaseBugFix.vcf.idx      |  Bin 2120 -> 2125 bytes
 ...tations.gatk3.7_30_ga4f720357.expected.vcf |   45 +-
 ...S_Annotations.keepRawCombined.expected.vcf |    3 +-
 ...o.20.21.gatk3.7_30_ga4f720357.expected.vcf |    2 -
 ...ngIndel.gatk3.7_30_ga4f720357.expected.vcf |    4 +-
 ...Trio.20.gatk3.7_30_ga4f720357.expected.vcf |  908 +++++++------
 ...Trio.21.gatk3.7_30_ga4f720357.expected.vcf | 1118 ++++++++---------
 .../ad-bug-gatk3.7_30_ga4f720357-output.vcf   |   20 +-
 ....bad.pl.gatk3.7_30_ga4f720357.expected.vcf |    4 +-
 ...exception.gatk3.7_30_ga4f720357.output.vcf |    4 +-
 .../expected.posteriors.genotyped.vcf         |  506 ++++----
 ...e.sample.pipeline.1.include_nonvariant.vcf |   14 +-
 ...e.sample.pipeline.2.include_nonvariant.vcf |    8 +-
 ...e.sample.pipeline.3.include_nonvariant.vcf |   10 +-
 ...gle.sample.pipeline.include_nonvariant.vcf |   16 +-
 ...epairResolution.includeNonVariantSites.vcf |   50 +-
 .../expected/includeLowQualSites.vcf          |    2 -
 .../expected/testSpanningDeletion.vcf         |    8 +-
 ...esolution.gatk3.7_30_ga4f720357.output.vcf |  138 +-
 ...xample1.gatk3.7_30_ga4f720357.expected.vcf |    7 +-
 .../GenotypeGVCFs/leadingDeletionExpected.vcf |    5 +-
 ...leadingDeletionRestrictToStartExpected.vcf |    5 +-
 ...lesTest.gatk3.7_30_ga4f720357.expected.vcf |  138 +-
 .../multiSamples.GATK3expected.g.vcf          |   11 +-
 ...ndaTest.gatk3.7_30_ga4f720357.expected.vcf |  138 +-
 .../newMQcalc.combined.genotyped.vcf          |    8 +-
 .../newMQcalc.combined.genotyped.vcf.idx      |  Bin 12199 -> 12204 bytes
 .../newMQcalc.singleSample.genotyped.vcf      |    4 +-
 ...ombined.gatk3.7_30_ga4f720357.expected.vcf |    5 +-
 ...delOnly.gatk3.7_30_ga4f720357.expected.vcf |    2 -
 ...delOnly.gatk3.7_30_ga4f720357.expected.vcf |    2 -
 ...onfTest.gatk3.7_30_ga4f720357.expected.vcf |  126 +-
 ...ificAnnotations.CombineGVCF.expected.g.vcf |   45 +-
 ...Annotations.CombineGVCF.expected.g.vcf.idx |  Bin 422 -> 506 bytes
 ...UpdatePGT.gatk3.7_30_ga4f720357.output.vcf |  138 +-
 60 files changed, 1758 insertions(+), 1794 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
index 4c2748ab422..6b1b7a02b88 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
@@ -282,7 +282,7 @@ public void apply(final Locatable loc, List<VariantContext> variants, ReadsConte
 
         if (regenotypedVC != null) {
             final SimpleInterval variantStart = new SimpleInterval(regenotypedVC.getContig(), regenotypedVC.getStart(), regenotypedVC.getStart());
-            if ((inForceOutputIntervals || !GATKVariantContextUtils.isSpanningDeletionOnly(regenotypedVC)) &&
+            if ((forceOutput || !GATKVariantContextUtils.isSpanningDeletionOnly(regenotypedVC)) &&
                     (!onlyOutputCallsStartingInIntervals || intervals.stream().anyMatch(interval -> interval.contains (variantStart)))) {
                 vcfWriter.add(regenotypedVC);
             }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
index cee67b5d716..18ff8d96ca5 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java
@@ -400,6 +400,7 @@ public VariantContextWriter setupVCFWriter(Set<VCFHeaderLine> defaultToolVCFHead
         if ( dbsnp.dbsnp != null  ) {
             VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
         }
+        headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
 
         final Set<String> sampleNameSet = samples.asSetOfSamples();
         outputHeader = new VCFHeader(headerLines, new TreeSet<>(sampleNameSet));
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java
index 24d88bd18cb..fd3666cd586 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java
@@ -86,7 +86,7 @@ private static int[] genotypeIndicesWithOnlyRefAndSpanDel(final int ploidy, fina
         } else {
             final int spanDelIndex = alleles.indexOf(Allele.SPAN_DEL);
             // allele counts are in the GenotypeLikelihoodCalculator format of {ref index, ref count, span del index, span del count}
-            return new IndexRange(0, ploidy).mapToInteger(n -> glCalc.alleleCountsToIndex(new int[]{0, ploidy - n, spanDelIndex, n}));
+            return new IndexRange(0, ploidy + 1).mapToInteger(n -> glCalc.alleleCountsToIndex(new int[]{0, ploidy - n, spanDelIndex, n}));
         }
     }
 
@@ -162,7 +162,7 @@ public AFCalculationResult calculate(final VariantContext vc, final int defaultP
             }
 
             // if the VC is biallelic the allele-specific qual equals the variant qual
-            if (numAlleles == 2) {
+            if (numAlleles == 2 && !spanningDeletionPresent) {
                 continue;
             }
 
@@ -183,7 +183,7 @@ public AFCalculationResult calculate(final VariantContext vc, final int defaultP
         }
 
         // for biallelic the allele-specific qual equals the variant qual, and we short-circuited the calculation above
-        if (numAlleles == 2) {
+        if (numAlleles == 2 && !spanningDeletionPresent) {
             log10POfZeroCountsByAllele[1] = log10PNoVariant;
         }
 
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
index 692ae9dce9c..c7cd169e820 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
@@ -44,6 +44,12 @@
 
 public class GenotypeGVCFsIntegrationTest extends CommandLineProgramTest {
 
+    // If true, update the expected outputs in tests that assert an exact match vs. prior output,
+    // instead of actually running the tests. Can be used with "./gradlew test -Dtest.single=GenotypeGVCFsIntegrationTest"
+    // to update all of the exact-match tests at once. After you do this, you should look at the
+    // diffs in the new expected outputs in git to confirm that they are consistent with expectations.
+    public static final boolean UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS = false;
+
     private static final List<String> NO_EXTRA_ARGS = Collections.emptyList();
      private static final String BASE_PAIR_EXPECTED = "gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf";
     private static final String b38_reference_20_21 = largeFileTestDir + "Homo_sapiens_assembly38.20.21.fasta";
@@ -163,6 +169,14 @@ public Object[][] GVCFsWithNewMQFormat() {
         };
     }
 
+    /*
+     * Make sure that someone didn't leave the UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS toggle turned on
+     */
+    @Test
+    public void assertThatExpectedOutputUpdateToggleIsDisabled() {
+        Assert.assertFalse(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS, "The toggle to update expected outputs should not be left enabled");
+    }
+
     /*
     This test is useful for testing changes in GATK4 versus different versions of GATK3.
     To use, set GATK3_PATH to point to a particular version of gatk, then enable this test and run.
@@ -354,12 +368,13 @@ private void runGenotypeGVCFSAndAssertSomething(File input, File expected, List<
     }
 
     private void runGenotypeGVCFSAndAssertSomething(String input, File expected, List<String> additionalArguments, BiConsumer<VariantContext, VariantContext> assertion, String reference) throws IOException {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected : createTempFile("genotypegvcf", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(reference))
                 .add("V", input)
                 .addFlag(RMSMappingQuality.RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT)
+                .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false)
                 .addOutput(output);
 
         additionalArguments.forEach(args::addRaw);
@@ -367,12 +382,14 @@ private void runGenotypeGVCFSAndAssertSomething(String input, File expected, Lis
         Utils.resetRandomGenerator();
         runCommandLine(args);
 
-        final List<VariantContext> expectedVC = VariantContextTestUtils.getVariantContexts(expected);
-        final List<VariantContext> actualVC = VariantContextTestUtils.getVariantContexts(output);
-        try {
-            assertForEachElementInLists(actualVC, expectedVC, assertion);
-        } catch (final AssertionError error) {
-            throw error;
+        if (! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS) {
+            final List<VariantContext> expectedVC = VariantContextTestUtils.getVariantContexts(expected);
+            final List<VariantContext> actualVC = VariantContextTestUtils.getVariantContexts(output);
+            try {
+                assertForEachElementInLists(actualVC, expectedVC, assertion);
+            } catch (final AssertionError error) {
+                throw error;
+            }
         }
     }
 
diff --git a/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf
index 4fea17ddf55..312f0f61768 100644
--- a/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:eb1959d5e5e527714f2002bd27d32fa1211d3ae684e7edd8a6c592a762df4cd8
-size 5488249
+oid sha256:704dc66a451f0912a50d394f60eb5eb62297aec83c76335dcf482ca58e6a17d6
+size 5486395
diff --git a/src/test/resources/large/gvcfs/gatk3.7_30_ga4f720357.24_sample.21.expected.vcf b/src/test/resources/large/gvcfs/gatk3.7_30_ga4f720357.24_sample.21.expected.vcf
index 0647ff71b62..a1119973c64 100644
--- a/src/test/resources/large/gvcfs/gatk3.7_30_ga4f720357.24_sample.21.expected.vcf
+++ b/src/test/resources/large/gvcfs/gatk3.7_30_ga4f720357.24_sample.21.expected.vcf
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a1f23f1a52de286d94d7aa961cbf7e85c3a89bbf8c1436c42abd6900e8e61333
-size 116849
+oid sha256:a5ad3879e068acfda76a40136407615db78184b87f0c02d57b54528a604785b3
+size 114932
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
index 2d7770e5717..38359adaa60 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf
@@ -916,7 +916,7 @@
 20	10068151	.	A	<NON_REF>	.	.	END=10068155	GT:DP:GQ:MIN_DP:PL	0/0:29:63:28:0,63,945
 20	10068156	.	A	<NON_REF>	.	.	END=10068157	GT:DP:GQ:MIN_DP:PL	0/0:27:57:27:0,57,855
 20	10068158	.	GTGTATATATATA	G,<NON_REF>	97.60	.	AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=5282.00|8882.00|0.00;AS_RAW_MQRankSum=|0.3,1|NaN;AS_RAW_ReadPosRankSum=|0.5,1|NaN;AS_SB_TABLE=0,3|2,2|0,0;BaseQRankSum=-0.842;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;RAW_MQandDP=89764,28;ReadPosRankSum=0.524	GT:AD:DP:GQ:PL:SB	0/1:3,4,0:7:57:105,0,57,114,69,183:0,3,2,2
-20	10068160	.	GTATATATATATGTA	G,*,<NON_REF>	88.01	.	AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|1682.00|8882.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|0,2|2,2|0,0;DP=32;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=101405,32	GT:AD:DP:GQ:PL:SB	1/2:0,2,4,0:6:53:706,158,131,98,0,53,489,171,104,458:0,0,2,4
+20	10068160	.	GTATATATATATGTA	G,*,<NON_REF>	56.01	.	AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|1682.00|8882.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|0,2|2,2|0,0;DP=32;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=101405,32	GT:AD:DP:GQ:PL:SB	1/2:0,2,4,0:6:53:706,158,131,98,0,53,489,171,104,458:0,0,2,4
 20	10068175	.	T	<NON_REF>	.	.	END=10068175	GT:DP:GQ:MIN_DP:PL	0/0:20:18:20:0,18,270
 20	10068176	.	A	<NON_REF>	.	.	END=10068180	GT:DP:GQ:MIN_DP:PL	0/0:19:24:17:0,24,360
 20	10068181	.	T	<NON_REF>	.	.	END=10068185	GT:DP:GQ:MIN_DP:PL	0/0:16:27:16:0,27,405
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx
index 2dff3244fecdebf10518f0204769483bf9291e17..68ef9ef6ebfd9a2b210eef2ee9165903a088cf30 100644
GIT binary patch
delta 49
zcmaF4kLkrerU_Eg$>kZTIf;4tF8Rr&xv6<2#rnzlDXIGDi6z++%^F!3@0)qMWaFN-
F^8f@?703Vp

delta 50
zcmaE{kLl$;rU_Cqskx~|m09{3sW~}Gsd*`>Mf&N9CE4-GIjM<x6HOag5A5E*uV~}$
GwetWV5EhL9

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
index 79ddd38820b..a809864f85a 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf
@@ -909,7 +909,7 @@
 20	10068151	.	A	<NON_REF>	.	.	END=10068155	GT:DP:GQ:MIN_DP:PL	0/0:29:63:28:0,63,945
 20	10068156	.	A	<NON_REF>	.	.	END=10068157	GT:DP:GQ:MIN_DP:PL	0/0:27:57:27:0,57,855
 20	10068158	.	GTGTATATATATA	G,<NON_REF>	97.60	.	BaseQRankSum=-0.842;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;RAW_MQandDP=89764,28;ReadPosRankSum=0.524	GT:AD:DP:GQ:PL:SB	0/1:3,4,0:7:57:105,0,57,114,69,183:0,3,2,2
-20	10068160	.	GTATATATATATGTA	G,*,<NON_REF>	88.01	.	DP=32;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=101405,32	GT:AD:DP:GQ:PL:SB	1/2:0,2,4,0:6:53:706,158,131,98,0,53,489,171,104,458:0,0,2,4
+20	10068160	.	GTATATATATATGTA	G,*,<NON_REF>	56.01	.	DP=32;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=101405,32	GT:AD:DP:GQ:PL:SB	1/2:0,2,4,0:6:53:706,158,131,98,0,53,489,171,104,458:0,0,2,4
 20	10068175	.	T	<NON_REF>	.	.	END=10068175	GT:DP:GQ:MIN_DP:PL	0/0:20:18:20:0,18,270
 20	10068176	.	A	<NON_REF>	.	.	END=10068180	GT:DP:GQ:MIN_DP:PL	0/0:19:24:17:0,24,360
 20	10068181	.	T	<NON_REF>	.	.	END=10068185	GT:DP:GQ:MIN_DP:PL	0/0:16:27:16:0,27,405
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx
index 970782130694876f595abbc54b2fd41d663ac447..b30840a3918cb806cbe3d86dd891ca59c3291761 100644
GIT binary patch
delta 49
zcmcb$kLl(<rU_Eg$>kZTIf;4tF8Rr&xv6<2#rnzlDXIGDi6z++&5Br$IL^FXvT^O&
Fc>wz(6)*q*

delta 50
zcmcb)kLlJvrU_Cqskx~|m09{3sW~}Gsd*`>Mf&N9CE4-GIjM<x6HSX)H5&KtE84hb
G?K}VyXBB?{

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testLinkedDebruijnMode.gatk4.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testLinkedDebruijnMode.gatk4.vcf
index 1befc171b5b..571a43fcde6 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testLinkedDebruijnMode.gatk4.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testLinkedDebruijnMode.gatk4.vcf
@@ -177,7 +177,7 @@
 20	10067264	.	G	A	2937.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=29.53;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0
 20	10067722	.	A	C	2161.06	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.63;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
 20	10068158	.	GTGTATATATATA	G	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.842;DP=28;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.62;MQRankSum=0.328;QD=13.94;ReadPosRankSum=0.524;SOR=0.061	GT:AD:DP:GQ:PL	0/1:3,4:7:57:105,0,57
-20	10068160	.	GTATATATATATGTA	G,*	88.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.29;QD=14.67;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53
+20	10068160	.	GTATATATATATGTA	G,*	56.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.29;QD=9.33;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53
 20	10068981	.	G	A	2528.06	.	AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.36;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2542,184,0
 20	10070602	.	T	C	2706.06	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.78;QD=28.13;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
 20	10070936	.	T	A	3646.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.96;QD=27.97;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3660,247,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testLinkedDebruijnMode.gatk4.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testLinkedDebruijnMode.gatk4.vcf.idx
index 50dc1009f6a2d7eddcf78f31c1c3a4858d94b071..f642716ebcf09168249d185777a2645cac5aae43 100644
GIT binary patch
delta 72
zcmew$_Fim)lyq`=MruxCp1w<da%paAUP-Zja(+sxetKd__C&KHUYAP@VDN@<*6osw
PTUT=lteprEfyn>>z#A6j

delta 73
zcmaDa_CaidluT-FYEfmDenx6ePEu-KN@|gQdSXd-d~!}|V%|j4B3{=^3}Eo$-u`_>
Q8@H_H5?D78A_9{E0RMLwYXATM

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf
index 051d1b3542d..5b6a2b281d0 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf
@@ -177,7 +177,7 @@
 20	10067264	.	G	A	2937.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=33.11;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0
 20	10067722	.	A	C	2161.06	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.20;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
 20	10068158	.	GTGTATATATATA	G	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.842;DP=28;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.62;MQRankSum=0.328;QD=13.94;ReadPosRankSum=0.524;SOR=0.061	GT:AD:DP:GQ:PL	0/1:3,4:7:57:105,0,57
-20	10068160	.	GTATATATATATGTA	G,*	88.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.29;QD=14.67;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53
+20	10068160	.	GTATATATATATGTA	G,*	56.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.29;QD=9.33;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53
 20	10068981	.	G	A	2518.06	.	AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.49;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0
 20	10070602	.	T	C	2706.06	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.78;QD=31.67;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
 20	10070936	.	T	A	3646.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.96;QD=29.53;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3660,247,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf
index 051d1b3542d..5b6a2b281d0 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf
@@ -177,7 +177,7 @@
 20	10067264	.	G	A	2937.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=33.11;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0
 20	10067722	.	A	C	2161.06	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.20;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
 20	10068158	.	GTGTATATATATA	G	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.842;DP=28;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.62;MQRankSum=0.328;QD=13.94;ReadPosRankSum=0.524;SOR=0.061	GT:AD:DP:GQ:PL	0/1:3,4:7:57:105,0,57
-20	10068160	.	GTATATATATATGTA	G,*	88.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.29;QD=14.67;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53
+20	10068160	.	GTATATATATATGTA	G,*	56.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.29;QD=9.33;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53
 20	10068981	.	G	A	2518.06	.	AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.49;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0
 20	10070602	.	T	C	2706.06	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.78;QD=31.67;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
 20	10070936	.	T	A	3646.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.96;QD=29.53;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3660,247,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx
index e77bc9ca248e7c9853ecde28f671f280a03b4ad1..b8aa2d078cdfa9106bdb2075be4fb7ffcb9d0d62 100644
GIT binary patch
delta 42
ycmaDX@IqjMlvr|kMruxCp1w<da%paAUP-Zja(+tcMD1+WYlj!#F4;Ky1Ump~jS>q0

delta 37
tcmaDM@K|7ilwfLZYEfmDenx6ePEu-KN@~$WgKX9dN;WTwH!e8A4geVr4^aRB

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx
index 07df04dab60c1a5ee269591224360f71931b9873..ad83853f3bafdcef22d2e19d3d6e6e194f929c9f 100644
GIT binary patch
delta 42
ycmew>)FeDXN-ViNBQ+;6Pv0d!ximL5ucTN%IX@+JqIMOl@6pA#OE#{$%mDyf&=F?<

delta 37
tcmZn?{wp*=N-#AywWu;nKO;3KCn+^ACADaxK^5x-C7Tz;8`odv000kn4>SM(

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx
index f92924617afe10f519463463d6f1ad77d122e63a..0fc3bb96e1e26513264a91a2447a32acd11016e0 100644
GIT binary patch
delta 44
zcmbPvhH2gzrU_DF$>kZTIf;4tF8Rr&xv6<2#rnzlDX9~+i&-_UFTP!}adFvF0F7M|
AwEzGB

delta 39
vcmbPthH2&*rU_Dlskx~|m09{3sW~}Gsd*`>MH3B*Sv&M>UKDR!QMMESI<XL0

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf.idx
index 69770df620a7eda12c96e2d5968b24595dcc7cf1..fd391a1996f8e335225e5c7d67ea1580296a7f25 100644
GIT binary patch
delta 41
xcmey$^owbNlvr|kMruxCp1w<da%paAUP-Zja(+tcMC~?Kza5KjmrUHY9{^S?5rzN&

delta 36
scmeyx^p$CXlwfLZYEfmDenx6ePEu-KN@~$WgErO|ayBoDC+^-401R*sa{vGU

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf.idx
index 2b07ec583cab2b36b3b6e91eed6c0b14c4bbdc08..1c79edc339a68b11b8875a4d9ed4095af2adeae6 100644
GIT binary patch
delta 44
zcmX?kkLlb!rU_DF$>kZTIf;4tF8Rr&xv6<2#rnzlDX9~+Ygk!NExui{an0Oy0HReB
AO8@`>

delta 39
vcmX?ikLlz+rU_Dlskx~|m09{3sW~}Gsd*`>MH3BbSa+z|yeQtdaqc<*P$&^c

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf.idx
index e568106711dd71613907a978e49485bf70efa51a..a4e0f7ef55b291c9bd0e3f437642785a8ae57eb8 100644
GIT binary patch
delta 44
zcmca`kLl_?rU_DF$>kZTIf;4tF8Rr&xv6<2#rnzlDX9~+n_1VLUVOV`<L0^R0ILHO
A5dZ)H

delta 39
vcmcb5kLkiarU_Dlskx~|m09{3sW~}Gsd*`>MH3C0S$C+}yeQtdW9~WtQkM~9

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx
index a496a9e76bc076847ffee41d109eb1aefb06d408..aed9b8b2daaf6e96f1d0214c799e513ba1b0f59c 100644
GIT binary patch
delta 44
zcmZ2{l4-?BrU_DF$>kZTIf;4tF8Rr&xv6<2#rnzlDX9~+t62RHExui{an;Yo0Fl!Z
AWB>pF

delta 39
vcmZ2+l4<ctrU_Dlskx~|m09{3sW~}Gsd*`>MH3CGST88qyeQtd{^w!<KvEGh

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx
index d9d78fecf4b167af1cc394a7802a300164eeb289..50eb1abd7279177b231b5f1ea113c748f7eb895c 100644
GIT binary patch
delta 42
ycmew;@J(QXlvr|kMruxCp1w<da%paAUP-Zja(+tcMC}sR_s16BF4?%`EIR;jiV|7?

delta 37
tcmew+@KIoblwfLZYEfmDenx6ePEu-KN@~$WgA&#qYBn#5H?BO(4geg^4{!hg

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx
index 3dbd1afc31c2a9f4caf5bd4dcbbc15e652012037..cbe30f1401ec34e954ff9a0567ff83e4b344682c 100644
GIT binary patch
delta 41
xcmdnMyp?%^lvr|kMruxCp1w<da%paAUP-Zja(+tcMC}gN>pK_UE}6LF2LMHi5yb!i

delta 36
scmdnWyn%UwlwfLZYEfmDenx6ePEu-KN@~$WgAUdgayBoDC+__L0QwjYC;$Ke

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx
index 0e87de3e0c927fd19a90af4157490e787c9e3c78..e9c7ac3d52e80216285a14745472a8ab2377e67f 100644
GIT binary patch
delta 41
xcmdnayoY&$lvr|kMruxCp1w<da%paAUP-Zja(+tcMD2c7%iW7_mrUIM0{}xT5k&w1

delta 36
scmdnPyq$T1lwfLZYEfmDenx6ePEu-KN@~$WgMQW*ayBoDCm#6$0Q^=DL;wH)

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx
index 733266e4121b0349df4ad9a80327090eab4a9818..5f871932947ad41b41a6b3db3b4bf595faa87d94 100644
GIT binary patch
delta 41
xcmdnRyq|f3lvr|kMruxCp1w<da%paAUP-Zja(+tcMD0neHG3A{E}3}f2LMK25tRS{

delta 36
scmdnbyo-5)lwfLZYEfmDenx6ePEu-KN@~$WgGsC}<ZNCPPdxqu0R2o4Pyhe`

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx
index 75cb142d2437de4d8326e1537f20e1d9aff04e1b..8758c813ba6190917c0c9aab1ba99424da284af0 100644
GIT binary patch
delta 42
ycmX>ha8_V~lvr|kMruxCp1w<da%paAUP-Zja(+tcMD1$U)Dw$umuy@;mmL6Jpb=gG

delta 37
tcmX>ra6({$lwfLZYEfmDenx6ePEu-KN@~$WgKE|tYBn#5H*T2A4ge8I4*UQB

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.gatk3.7_30_ga4f720357.expected.vcf
index c9e1f66ebd1..ab2e1a2ddde 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.gatk3.7_30_ga4f720357.expected.vcf
@@ -12,12 +12,12 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:39:50 EDT 2017",Epoch=1498567190652,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/Users/gauthier/workspaces/gsa-unstable/private/gatk-tools-private/src/test/resources//NA12878.HiSeq.b37.chr20.10_11mb.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf3705275068409322120.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --annotation ClippingRankSumTest --annotation-group AS_StandardAnnotation --annotation-group StandardAnnotation --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="August 2, 2019 3:55:25 PM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
 ##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
 ##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
 ##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient">
 ##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
 ##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
@@ -133,29 +133,28 @@
 ##contig=<ID=GL000192.1,length=547496>
 ##contig=<ID=NC_007605,length=171823>
 ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10087820	.	C	CAG	294.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.100;AS_FS=2.811;AS_MQ=60.00;AS_MQRankSum=0.600;AS_QD=6.15;AS_ReadPosRankSum=-0.400;AS_SOR=1.147;BaseQRankSum=-2.273e+00;DP=93;ExcessHet=3.0103;FS=4.432;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.678;QD=6.14;RAW_MQ=329810.00;ReadPosRankSum=-4.920e-01;SOR=1.302	GT:AD:GQ:PL	0/1:35,13:99:302,0,1079
-20	10433322	.	A	AT	116.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.500;AS_FS=0.000;AS_MQ=44.10;AS_MQRankSum=1.100;AS_QD=7.31;AS_ReadPosRankSum=2.000;AS_SOR=0.836;BaseQRankSum=2.56;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.98;MQRankSum=1.12;QD=7.29;RAW_MQ=67710.00;ReadPosRankSum=2.04;SOR=0.836	GT:AD:GQ:PL	0/1:11,5:99:124,0,369
-20	10433324	.	A	T	220.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.200;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_QD=15.79;AS_ReadPosRankSum=1.500;AS_SOR=0.412;BaseQRankSum=2.28;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.82;MQRankSum=0.584;QD=15.76;RAW_MQ=60510.00;ReadPosRankSum=1.54;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
-20	10433326	.	A	T	220.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.800;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_QD=15.79;AS_ReadPosRankSum=1.400;AS_SOR=0.412;BaseQRankSum=0.874;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.47;MQRankSum=0.584;QD=15.76;RAW_MQ=53310.00;ReadPosRankSum=1.40;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
+20	10087820	.	C	CAG	294.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.100;AS_FS=2.811;AS_MQ=60.00;AS_MQRankSum=0.600;AS_QD=6.15;AS_ReadPosRankSum=-0.400;AS_SOR=1.147;BaseQRankSum=-2.273e+00;DP=93;ExcessHet=3.0103;FS=4.432;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.678;QD=6.14;RAW_MQ=329810.00;ReadPosRankSum=-4.920e-01;SOR=1.302	GT:AD:GQ:PL	0/1:35,13:99:302,0,1079
+20	10433322	.	A	AT	116.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.500;AS_FS=0.000;AS_MQ=44.10;AS_MQRankSum=1.100;AS_QD=7.31;AS_ReadPosRankSum=2.000;AS_SOR=0.836;BaseQRankSum=2.56;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.98;MQRankSum=1.12;QD=7.29;RAW_MQ=67710.00;ReadPosRankSum=2.04;SOR=0.836	GT:AD:GQ:PL	0/1:11,5:99:124,0,369
+20	10433324	.	A	T	220.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.200;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_QD=15.79;AS_ReadPosRankSum=1.500;AS_SOR=0.412;BaseQRankSum=2.28;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.82;MQRankSum=0.584;QD=15.76;RAW_MQ=60510.00;ReadPosRankSum=1.54;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
+20	10433326	.	A	T	220.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.800;AS_FS=0.000;AS_MQ=41.96;AS_MQRankSum=0.500;AS_QD=15.79;AS_ReadPosRankSum=1.400;AS_SOR=0.412;BaseQRankSum=0.874;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.47;MQRankSum=0.584;QD=15.76;RAW_MQ=53310.00;ReadPosRankSum=1.40;SOR=0.412	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275
 20	10433328	.	A	T,ATATAT	902.06	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=.,.;AS_FS=0.000,0.000;AS_MQ=41.96,29.00;AS_MQRankSum=.,.;AS_QD=25.36,28.73;AS_ReadPosRankSum=.,.;AS_SOR=1.329,1.179;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.71;QD=30.97;RAW_MQ=49710.00;SOR=1.402	GT:AD:GQ:PL	1/2:0,6,3:99:919,177,246,420,0,500
-20	10433382	.	T	C	624.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.900;AS_FS=0.000;AS_MQ=55.21;AS_MQRankSum=1.000;AS_QD=20.83;AS_ReadPosRankSum=0.200;AS_SOR=0.998;BaseQRankSum=-1.821e+00;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=1.03;QD=20.82;RAW_MQ=86585.00;ReadPosRankSum=0.249;SOR=0.998	GT:AD:GQ:PGT:PID:PL	0/1:15,15:99:0|1:10433382_T_C:632,0,601
-20	10433391	.	T	C	623.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.300;AS_FS=0.000;AS_MQ=57.05;AS_MQRankSum=1.300;AS_QD=18.35;AS_ReadPosRankSum=1.500;AS_SOR=0.859;BaseQRankSum=-2.840e-01;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQRankSum=1.33;QD=18.34;RAW_MQ=103744.00;ReadPosRankSum=1.54;SOR=0.859	GT:AD:GQ:PGT:PID:PL	0/1:18,16:99:0|1:10433382_T_C:631,0,673
-20	10433468	.	T	C	645.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.955;AS_MQ=58.84;AS_MQRankSum=0.000;AS_QD=17.00;AS_ReadPosRankSum=1.400;AS_SOR=0.324;BaseQRankSum=-1.312e+00;DP=38;ExcessHet=3.0103;FS=2.955;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=0.076;QD=16.99;RAW_MQ=132290.00;ReadPosRankSum=1.46;SOR=0.324	GT:AD:GQ:PL	0/1:18,20:99:653,0,572
-20	10433560	.	C	A	987.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.400;AS_FS=5.027;AS_MQ=59.25;AS_MQRankSum=-1.100;AS_QD=17.64;AS_ReadPosRankSum=1.300;AS_SOR=0.129;BaseQRankSum=3.50;DP=56;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=-1.078e+00;QD=17.64;RAW_MQ=199369.00;ReadPosRankSum=1.38;SOR=0.129	GT:AD:GQ:PGT:PID:PL	0/1:31,25:99:0|1:10433560_C_A:995,0,3032
-20	10433575	.	C	T	1143.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.800;AS_FS=1.568;AS_MQ=57.81;AS_MQRankSum=-1.200;AS_QD=17.88;AS_ReadPosRankSum=0.800;AS_SOR=0.375;BaseQRankSum=3.81;DP=64;ExcessHet=3.0103;FS=1.568;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=-1.123e+00;QD=17.87;RAW_MQ=219892.00;ReadPosRankSum=0.830;SOR=0.375	GT:AD:GQ:PGT:PID:PL	0/1:34,30:99:0|1:10433560_C_A:1151,0,3385
-20	10433594	.	C	T	1105.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=4.800;AS_FS=1.535;AS_MQ=54.33;AS_MQRankSum=-2.400;AS_QD=18.43;AS_ReadPosRankSum=-0.600;AS_SOR=0.415;BaseQRankSum=4.82;DP=61;ExcessHet=3.0103;FS=1.535;MLEAC=1;MLEAF=0.500;MQ=56.66;MQRankSum=-2.334e+00;QD=18.43;RAW_MQ=195825.00;ReadPosRankSum=-5.020e-01;SOR=0.415	GT:AD:GQ:PGT:PID:PL	0/1:31,29:99:0|1:10433560_C_A:1113,0,3070
-20	10433809	.	A	G	1135.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.400;AS_FS=0.968;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=17.21;AS_ReadPosRankSum=-0.500;AS_SOR=0.930;BaseQRankSum=1.41;DP=68;ExcessHet=3.0103;FS=0.968;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.00;QD=17.21;RAW_MQ=242569.00;ReadPosRankSum=-4.450e-01;SOR=0.930	GT:AD:GQ:PL	0/1:32,34:99:1143,0,1041
-20	10433955	.	C	CGTGTGTGTGTAT	1027.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_MQ=40.57;AS_MQRankSum=-4.000;AS_QD=24.48;AS_ReadPosRankSum=-0.800;AS_SOR=0.710;BaseQRankSum=0.422;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQRankSum=-4.001e+00;QD=24.47;RAW_MQ=117307.00;ReadPosRankSum=-7.890e-01;SOR=0.710	GT:AD:GQ:PL	0/1:18,24:99:1035,0,1217
-20	10434177	.	A	T	1467.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.900;AS_FS=0.888;AS_MQ=55.78;AS_MQRankSum=-2.500;AS_QD=20.11;AS_ReadPosRankSum=-0.900;AS_SOR=0.836;BaseQRankSum=0.903;DP=74;ExcessHet=3.0103;FS=0.888;MLEAC=1;MLEAF=0.500;MQ=57.58;MQRankSum=-2.473e+00;QD=20.10;RAW_MQ=245384.00;ReadPosRankSum=-8.910e-01;SOR=0.836	GT:AD:GQ:PL	0/1:30,43:99:1475,0,936
-20	10434258	.	G	A	1235.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.000;AS_FS=0.000;AS_MQ=52.93;AS_MQRankSum=-2.900;AS_QD=17.91;AS_ReadPosRankSum=-0.200;AS_SOR=0.776;BaseQRankSum=3.06;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.99;MQRankSum=-2.871e+00;QD=17.91;RAW_MQ=219420.00;ReadPosRankSum=-1.550e-01;SOR=0.776	GT:AD:GQ:PL	0/1:31,38:99:1243,0,1003
+20	10433382	.	T	C	624.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.900;AS_FS=0.000;AS_MQ=55.21;AS_MQRankSum=1.000;AS_QD=20.83;AS_ReadPosRankSum=0.200;AS_SOR=0.998;BaseQRankSum=-1.821e+00;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=1.03;QD=20.82;RAW_MQ=86585.00;ReadPosRankSum=0.249;SOR=0.998	GT:AD:GQ:PGT:PID:PL	0/1:15,15:99:0|1:10433382_T_C:632,0,601
+20	10433391	.	T	C	623.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.300;AS_FS=0.000;AS_MQ=57.05;AS_MQRankSum=1.300;AS_QD=18.35;AS_ReadPosRankSum=1.500;AS_SOR=0.859;BaseQRankSum=-2.840e-01;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQRankSum=1.33;QD=18.34;RAW_MQ=103744.00;ReadPosRankSum=1.54;SOR=0.859	GT:AD:GQ:PGT:PID:PL	0/1:18,16:99:0|1:10433382_T_C:631,0,673
+20	10433468	.	T	C	645.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.955;AS_MQ=58.84;AS_MQRankSum=0.000;AS_QD=17.00;AS_ReadPosRankSum=1.400;AS_SOR=0.324;BaseQRankSum=-1.312e+00;DP=38;ExcessHet=3.0103;FS=2.955;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=0.076;QD=16.99;RAW_MQ=132290.00;ReadPosRankSum=1.46;SOR=0.324	GT:AD:GQ:PL	0/1:18,20:99:653,0,572
+20	10433560	.	C	A	987.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.400;AS_FS=5.027;AS_MQ=59.25;AS_MQRankSum=-1.100;AS_QD=17.64;AS_ReadPosRankSum=1.300;AS_SOR=0.129;BaseQRankSum=3.50;DP=56;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=-1.078e+00;QD=17.64;RAW_MQ=199369.00;ReadPosRankSum=1.38;SOR=0.129	GT:AD:GQ:PGT:PID:PL	0/1:31,25:99:0|1:10433560_C_A:995,0,3032
+20	10433575	.	C	T	1143.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.800;AS_FS=1.568;AS_MQ=57.81;AS_MQRankSum=-1.200;AS_QD=17.88;AS_ReadPosRankSum=0.800;AS_SOR=0.375;BaseQRankSum=3.81;DP=64;ExcessHet=3.0103;FS=1.568;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=-1.123e+00;QD=17.87;RAW_MQ=219892.00;ReadPosRankSum=0.830;SOR=0.375	GT:AD:GQ:PGT:PID:PL	0/1:34,30:99:0|1:10433560_C_A:1151,0,3385
+20	10433594	.	C	T	1105.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=4.800;AS_FS=1.535;AS_MQ=54.33;AS_MQRankSum=-2.400;AS_QD=18.43;AS_ReadPosRankSum=-0.600;AS_SOR=0.415;BaseQRankSum=4.82;DP=61;ExcessHet=3.0103;FS=1.535;MLEAC=1;MLEAF=0.500;MQ=56.66;MQRankSum=-2.334e+00;QD=18.43;RAW_MQ=195825.00;ReadPosRankSum=-5.020e-01;SOR=0.415	GT:AD:GQ:PGT:PID:PL	0/1:31,29:99:0|1:10433560_C_A:1113,0,3070
+20	10433809	.	A	G	1135.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=1.400;AS_FS=0.968;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=17.21;AS_ReadPosRankSum=-0.500;AS_SOR=0.930;BaseQRankSum=1.41;DP=68;ExcessHet=3.0103;FS=0.968;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.00;QD=17.21;RAW_MQ=242569.00;ReadPosRankSum=-4.450e-01;SOR=0.930	GT:AD:GQ:PL	0/1:32,34:99:1143,0,1041
+20	10433955	.	C	CGTGTGTGTGTAT	1027.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_MQ=40.57;AS_MQRankSum=-4.000;AS_QD=24.48;AS_ReadPosRankSum=-0.800;AS_SOR=0.710;BaseQRankSum=0.422;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQRankSum=-4.001e+00;QD=24.47;RAW_MQ=117307.00;ReadPosRankSum=-7.890e-01;SOR=0.710	GT:AD:GQ:PL	0/1:18,24:99:1035,0,1217
+20	10434177	.	A	T	1467.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=0.900;AS_FS=0.888;AS_MQ=55.78;AS_MQRankSum=-2.500;AS_QD=20.11;AS_ReadPosRankSum=-0.900;AS_SOR=0.836;BaseQRankSum=0.903;DP=74;ExcessHet=3.0103;FS=0.888;MLEAC=1;MLEAF=0.500;MQ=57.58;MQRankSum=-2.473e+00;QD=20.10;RAW_MQ=245384.00;ReadPosRankSum=-8.910e-01;SOR=0.836	GT:AD:GQ:PL	0/1:30,43:99:1475,0,936
+20	10434258	.	G	A	1235.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=3.000;AS_FS=0.000;AS_MQ=52.93;AS_MQRankSum=-2.900;AS_QD=17.91;AS_ReadPosRankSum=-0.200;AS_SOR=0.776;BaseQRankSum=3.06;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.99;MQRankSum=-2.871e+00;QD=17.91;RAW_MQ=219420.00;ReadPosRankSum=-1.550e-01;SOR=0.776	GT:AD:GQ:PL	0/1:31,38:99:1243,0,1003
 20	10434384	.	TA	T	782.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.100;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=1.000;AS_QD=11.51;AS_ReadPosRankSum=0.400;AS_SOR=0.723;BaseQRankSum=-1.000e-01;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=1.00;QD=11.51;RAW_MQ=253369.00;ReadPosRankSum=0.497;SOR=0.723	GT:AD:GQ:PL	0/1:35,33:99:790,0,846
-20	10434519	.	T	C	1464.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.200;AS_FS=1.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.78;AS_ReadPosRankSum=-0.800;AS_SOR=0.900;BaseQRankSum=-3.137e+00;DP=78;ExcessHet=3.0103;FS=1.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.78;RAW_MQ=280800.00;ReadPosRankSum=-7.490e-01;SOR=0.900	GT:AD:GQ:PL	0/1:35,43:99:1472,0,1192
+20	10434519	.	T	C	1464.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-3.200;AS_FS=1.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.78;AS_ReadPosRankSum=-0.800;AS_SOR=0.900;BaseQRankSum=-3.137e+00;DP=78;ExcessHet=3.0103;FS=1.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.78;RAW_MQ=280800.00;ReadPosRankSum=-7.490e-01;SOR=0.900	GT:AD:GQ:PL	0/1:35,43:99:1472,0,1192
 20	10435067	.	GTA	G	1446.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.600;AS_FS=3.289;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=21.60;AS_ReadPosRankSum=-0.200;AS_SOR=1.121;BaseQRankSum=2.60;DP=67;ExcessHet=3.0103;FS=3.289;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.59;RAW_MQ=241200.00;ReadPosRankSum=-1.830e-01;SOR=1.121	GT:AD:GQ:PL	0/1:30,37:99:1454,0,1191
-20	10435948	.	A	C	1137.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.700;AS_FS=3.002;AS_MQ=54.65;AS_MQRankSum=-3.200;AS_QD=14.97;AS_ReadPosRankSum=-1.600;AS_SOR=0.855;BaseQRankSum=-4.692e+00;DP=76;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.500;MQ=57.53;MQRankSum=-3.121e+00;QD=14.97;RAW_MQ=251528.00;ReadPosRankSum=-1.594e+00;SOR=0.855	GT:AD:GQ:PL	0/1:40,36:99:1145,0,1413
-20	10436227	.	TTTTATTTATTTATTTATTTA	T,TTTTATTTATTTATTTATTTATTTA	1208.06	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=.,.;AS_FS=0.000,0.000;AS_MQ=32.72,53.03;AS_MQRankSum=.,.;AS_QD=27.24,28.88;AS_ReadPosRankSum=.,.;AS_SOR=0.382,0.330;BaseQRankSum=-1.450e+00;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.77;MQRankSum=-1.660e+00;QD=28.20;RAW_MQ=201025.00;ReadPosRankSum=1.30;SOR=0.379	GT:AD:GQ:PL	1/2:1,24,7:99:1225,241,589,947,0,970
-20	10436415	.	A	G	1190.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.800;AS_FS=9.312;AS_MQ=59.42;AS_MQRankSum=0.400;AS_QD=18.90;AS_ReadPosRankSum=-0.100;AS_SOR=0.739;BaseQRankSum=-2.775e+00;DP=63;ExcessHet=3.0103;FS=9.312;MLEAC=1;MLEAF=0.500;MQ=59.51;MQRankSum=0.399;QD=18.90;RAW_MQ=223145.00;ReadPosRankSum=-6.300e-02;SOR=0.739	GT:AD:GQ:PL	0/1:23,40:99:1198,0,691
-20	10436582	.	A	G	1187.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=3.189;AS_MQ=52.86;AS_MQRankSum=-2.700;AS_QD=16.73;AS_ReadPosRankSum=0.200;AS_SOR=0.906;BaseQRankSum=-1.326e+00;DP=71;ExcessHet=3.0103;FS=3.189;MLEAC=1;MLEAF=0.500;MQ=55.76;MQRankSum=-2.639e+00;QD=16.73;RAW_MQ=220789.00;ReadPosRankSum=0.267;SOR=0.906	GT:AD:GQ:PL	0/1:34,37:99:1195,0,1113
-20	10436700	.	A	G	1333.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.012;AS_MQ=59.53;AS_MQRankSum=-0.900;AS_QD=19.06;AS_ReadPosRankSum=0.500;AS_SOR=0.449;BaseQRankSum=-1.329e+00;DP=70;ExcessHet=3.0103;FS=2.012;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-8.370e-01;QD=19.05;RAW_MQ=249769.00;ReadPosRankSum=0.581;SOR=0.449	GT:AD:GQ:PL	0/1:30,40:99:1341,0,961
-20	10436908	.	C	G	1361.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.900;AS_FS=4.557;AS_MQ=58.89;AS_MQRankSum=-1.000;AS_QD=16.41;AS_ReadPosRankSum=-0.200;AS_SOR=1.252;BaseQRankSum=-8.440e-01;DP=83;ExcessHet=3.0103;FS=4.557;MLEAC=1;MLEAF=0.500;MQ=59.26;MQRankSum=-9.940e-01;QD=16.40;RAW_MQ=291487.00;ReadPosRankSum=-1.480e-01;SOR=1.252	GT:AD:GQ:PL	0/1:41,42:99:1369,0,1378
+20	10435948	.	A	C	1137.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-4.700;AS_FS=3.002;AS_MQ=54.65;AS_MQRankSum=-3.200;AS_QD=14.97;AS_ReadPosRankSum=-1.600;AS_SOR=0.855;BaseQRankSum=-4.692e+00;DP=76;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.500;MQ=57.53;MQRankSum=-3.121e+00;QD=14.97;RAW_MQ=251528.00;ReadPosRankSum=-1.594e+00;SOR=0.855	GT:AD:GQ:PL	0/1:40,36:99:1145,0,1413
+20	10436227	.	TTTTATTTATTTATTTATTTA	T,TTTTATTTATTTATTTATTTATTTA	1208.02	.	AC=1,1;AF=0.500,0.500;AN=2;AS_BaseQRankSum=.,.;AS_FS=0.000,0.000;AS_MQ=32.72,53.03;AS_MQRankSum=.,.;AS_QD=27.24,28.88;AS_ReadPosRankSum=.,.;AS_SOR=0.382,0.330;BaseQRankSum=-1.450e+00;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.77;MQRankSum=-1.660e+00;QD=28.20;RAW_MQ=201025.00;ReadPosRankSum=1.30;SOR=0.379	GT:AD:GQ:PL	1/2:1,24,7:99:1225,241,589,947,0,970
+20	10436415	.	A	G	1190.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.800;AS_FS=9.312;AS_MQ=59.42;AS_MQRankSum=0.400;AS_QD=18.90;AS_ReadPosRankSum=-0.100;AS_SOR=0.739;BaseQRankSum=-2.775e+00;DP=63;ExcessHet=3.0103;FS=9.312;MLEAC=1;MLEAF=0.500;MQ=59.51;MQRankSum=0.399;QD=18.90;RAW_MQ=223145.00;ReadPosRankSum=-6.300e-02;SOR=0.739	GT:AD:GQ:PL	0/1:23,40:99:1198,0,691
+20	10436582	.	A	G	1187.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=3.189;AS_MQ=52.86;AS_MQRankSum=-2.700;AS_QD=16.73;AS_ReadPosRankSum=0.200;AS_SOR=0.906;BaseQRankSum=-1.326e+00;DP=71;ExcessHet=3.0103;FS=3.189;MLEAC=1;MLEAF=0.500;MQ=55.76;MQRankSum=-2.639e+00;QD=16.73;RAW_MQ=220789.00;ReadPosRankSum=0.267;SOR=0.906	GT:AD:GQ:PL	0/1:34,37:99:1195,0,1113
+20	10436700	.	A	G	1333.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-1.400;AS_FS=2.012;AS_MQ=59.53;AS_MQRankSum=-0.900;AS_QD=19.06;AS_ReadPosRankSum=0.500;AS_SOR=0.449;BaseQRankSum=-1.329e+00;DP=70;ExcessHet=3.0103;FS=2.012;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-8.370e-01;QD=19.05;RAW_MQ=249769.00;ReadPosRankSum=0.581;SOR=0.449	GT:AD:GQ:PL	0/1:30,40:99:1341,0,961
+20	10436908	.	C	G	1361.64	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-0.900;AS_FS=4.557;AS_MQ=58.89;AS_MQRankSum=-1.000;AS_QD=16.41;AS_ReadPosRankSum=-0.200;AS_SOR=1.252;BaseQRankSum=-8.440e-01;DP=83;ExcessHet=3.0103;FS=4.557;MLEAC=1;MLEAF=0.500;MQ=59.26;MQRankSum=-9.940e-01;QD=16.41;RAW_MQ=291487.00;ReadPosRankSum=-1.480e-01;SOR=1.252	GT:AD:GQ:PL	0/1:41,42:99:1369,0,1378
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf
index 5b95e3ea35a..aaa2259f1a8 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/AS_Annotations.keepRawCombined.expected.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:39:50 EDT 2017",Epoch=1498567190652,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/Users/gauthier/workspaces/gsa-unstable/private/gatk-tools-private/src/test/resources//NA12878.HiSeq.b37.chr20.10_11mb.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/56/l8cj86792b773xql3374k3dcmtd1k5/T/genotypegvcf5322964147609906403.vcf --keep-combined-raw-annotations true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/NA12878.AS.chr20snippet.g.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --annotation ClippingRankSumTest --annotation-group AS_StandardAnnotation --annotation-group StandardAnnotation --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="January 21, 2020 1:45:44 PM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -34,6 +33,7 @@
 ##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
 ##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
 ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
 ##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
 ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
 ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
@@ -139,7 +139,6 @@
 ##contig=<ID=GL000192.1,length=547496>
 ##contig=<ID=NC_007605,length=171823>
 ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 20	10087820	.	C	CAG	294.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=-2.100;AS_FS=2.811;AS_MQ=60.00;AS_MQRankSum=0.600;AS_QD=6.15;AS_QUAL=295;AS_RAW_BaseQRankSum=|-2.1,1;AS_RAW_MQ=123769.00|46800.00;AS_RAW_MQRankSum=|0.6,1;AS_RAW_ReadPosRankSum=|-0.4,1;AS_ReadPosRankSum=-0.400;AS_SB_TABLE=17,18|8,5;AS_SOR=1.147;BaseQRankSum=-2.273e+00;DP=93;ExcessHet=3.0103;FS=4.432;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.678;QD=6.14;RAW_MQ=329810.00;ReadPosRankSum=-4.920e-01;SOR=1.302	GT:AD:GQ:PL	0/1:35,13:99:302,0,1079
 20	10433322	.	A	AT	116.60	.	AC=1;AF=0.500;AN=2;AS_BaseQRankSum=2.500;AS_FS=0.000;AS_MQ=44.10;AS_MQRankSum=1.100;AS_QD=7.31;AS_QUAL=117;AS_RAW_BaseQRankSum=|2.5,1;AS_RAW_MQ=14418.00|9723.00;AS_RAW_MQRankSum=|1.1,1;AS_RAW_ReadPosRankSum=|2.0,1;AS_ReadPosRankSum=2.000;AS_SB_TABLE=5,6|2,3;AS_SOR=0.836;BaseQRankSum=2.56;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.98;MQRankSum=1.12;QD=7.29;RAW_MQ=67710.00;ReadPosRankSum=2.04;SOR=0.836	GT:AD:GQ:PL	0/1:11,5:99:124,0,369
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf
index 731d947779a..64d4087cb37 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Thu Jun 09 17:26:25 EDT 2016",Epoch=1465507585958,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=src/test/resources/large/human_g1k_v37.20.21.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf --dbsnp /Users/ckachuli/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf --variant src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf --reference src/test/resources/large/human_g1k_v37.20.21.fasta --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-vcf-codec false --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.6.0-3-g63155f6-SNAPSHOT",Date="June 4, 2020 5:03:05 PM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -36,7 +35,6 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/louisb/Workspace/gatk-protected/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 20	9999996	.	A	ACT	3799.03	.	AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.44;QD=25.36;SOR=1.075	GT:AD:DP:GQ:PL	1/1:0,84:84:99:3813,256,0
 20	10000117	rs4816203	C	T	926.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=-2.551e+00;DB;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-2.370e-01;QD=14.48;ReadPosRankSum=1.01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf
index d1743a9b619..eb3cc379fdc 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Thu Jun 09 17:26:25 EDT 2016",Epoch=1465507585958,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=src/test/resources/large/human_g1k_v37.20.21.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf --dbsnp /Users/davidben/broad/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.21.missingIndel.g.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:17 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -36,6 +35,5 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/louisb/Workspace/gatk-protected/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10156378	rs35304411	A	AT	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.850e-01;ClippingRankSum=-1.900e-02;DB;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=-1.159e+00;QD=3.86;ReadPosRankSum=0.218;SOR=0.807	GT:AD:DP:GQ:PL	0/1:14,10:32:99:100,0,285
+20	10156378	rs35304411	A	AT	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.850e-01;ClippingRankSum=-1.900e-02;DB;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=-1.159e+00;QD=3.86;ReadPosRankSum=0.218;SOR=0.807	GT:AD:DP:GQ:PL	0/1:14,10:32:99:100,0,285
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf
index 6dd3eb653ac..b4fadd61388 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf
@@ -13,8 +13,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Thu Jun 09 17:26:25 EDT 2016",Epoch=1465507585958,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=src/test/resources/large/human_g1k_v37.20.21.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport  --genomicsdb-workspace-path /var/folders/56/l8cj86792b773xql3374k3dcmtd1k5/T/genomicsDBWorkspace2631700463525622330/workspace --variant /Users/davidben/broad/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf --intervals 20:1-11000000 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --batch-size 0 --consolidate false --validate-sample-name-map false --merge-input-intervals false --reader-threads 1 --max-num-intervals-to-import-in-parallel 1 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=Unavailable,Date="January 27, 2019 1:18:26 AM EST">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf --variant gendb:///var/folders/56/l8cj86792b773xql3374k3dcmtd1k5/T/genomicsDBWorkspace2631700463525622330/workspace --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:18:27 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -37,501 +35,499 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/louisb/Workspace/gatk-protected/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenomicsDBImport
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	9999996	.	A	ACT	3799.06	.	AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.44;QD=25.36;SOR=1.075	GT:AD:DP:GQ:PL	1/1:0,84:84:99:3813,256,0
-20	10000117	.	C	T	926.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=-2.551e+00;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-2.370e-01;QD=14.48;ReadPosRankSum=1.01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
-20	10000211	.	C	T	962.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.84;ClippingRankSum=-1.201e+00;DP=54;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-5.600e-01;QD=18.16;ReadPosRankSum=1.72;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
-20	10000439	.	T	G	2819.03	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=28.73;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0
-20	10000598	.	T	A	1956.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=30.97;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0
-20	10000694	.	G	A	1029.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.57;ClippingRankSum=0.093;DP=82;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.66;MQRankSum=-4.109e+00;QD=12.56;ReadPosRankSum=1.14;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601
-20	10000758	.	T	A	3853.03	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=27.24;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0
-20	10001019	.	T	G	671.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.069e+00;ClippingRankSum=0.408;DP=65;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=49.49;MQRankSum=-6.448e+00;QD=10.33;ReadPosRankSum=-6.900e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426
-20	10001298	.	T	A	2932.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=28.20;SOR=0.963	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0
-20	10001436	.	A	AAGGCT	2325.06	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.88;QD=25.00;SOR=3.442	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2339,156,0
-20	10001474	.	C	T	2655.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;QD=29.56;SOR=1.516	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0
-20	10001617	.	C	A	1752.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.15;ClippingRankSum=-4.120e-01;DP=103;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-2.140e-01;QD=17.02;ReadPosRankSum=0.557;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781
-20	10001628	.	G	A	3913.03	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=30.62;SOR=1.053	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0
-20	10001661	.	T	C	3621.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=28.17;SOR=1.193	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0
-20	10001670	.	T	G	3688.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=26.80;SOR=0.995	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0
-20	10002058	.	T	G	2978.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.69;ClippingRankSum=0.577;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;MQRankSum=1.41;QD=26.00;ReadPosRankSum=0.762;SOR=0.776	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0
-20	10002099	.	C	T	1215.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;ClippingRankSum=0.020;DP=66;ExcessHet=3.0103;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-8.590e-01;QD=18.70;ReadPosRankSum=-3.660e-01;SOR=0.375	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844
-20	10002138	.	C	G	2458.03	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.38;QD=30.02;SOR=0.730	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0
-20	10002142	.	G	C	2422.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.31;QD=31.98;SOR=0.853	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,52:52:99:1|1:10002138_C_G:2436,166,0
-20	10002458	.	G	GTTT	2155.04	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.07;QD=27.51;SOR=2.049	GT:AD:DP:GQ:PL	1/1:0,6:16:99:2090,167,0
-20	10002470	.	C	T	2537.03	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;QD=29.11;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2551,189,0
-20	10002625	.	G	T	2680.03	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=28.08;SOR=1.127	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0
-20	10003021	.	C	T	2398.03	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;QD=23.23;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0
-20	10003358	.	A	C	1475.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;ClippingRankSum=0.513;DP=90;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=-3.700e-02;QD=16.58;ReadPosRankSum=0.078;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477
-20	10003651	.	T	C	3635.03	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=29.03;SOR=1.511	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0
-20	10003692	.	A	G	2624.03	.	AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=30.67;SOR=1.352	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0
-20	10003832	.	G	A	2720.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;QD=26.61;SOR=1.473	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0
-20	10004094	.	A	C	1840.03	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;QD=34.72;SOR=1.524	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0
-20	10004147	.	A	G	1852.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;QD=29.20;SOR=1.136	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0
-20	10004193	.	G	T	939.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.000e-01;ClippingRankSum=-1.110e-01;DP=53;ExcessHet=3.0103;FS=2.391;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=3.46;QD=18.07;ReadPosRankSum=0.737;SOR=1.019	GT:AD:DP:GQ:PL	0/1:23,29:52:99:947,0,775
-20	10004222	.	C	CA	42.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.157;ClippingRankSum=0.122;DP=55;ExcessHet=3.0103;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.05;MQRankSum=-2.139e+00;QD=1.09;ReadPosRankSum=-5.200e-02;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,8:39:50:50,0,923
-20	10004223	.	A	AG	77.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.650e-01;ClippingRankSum=0.289;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQRankSum=1.50;QD=1.65;ReadPosRankSum=2.12;SOR=0.638	GT:AD:DP:GQ:PL	0/1:36,11:47:85:85,0,982
-20	10004351	.	C	G	2770.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=28.55;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2784,211,0
-20	10004389	.	T	G	2509.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;QD=34.42;SOR=1.143	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0
-20	10004610	.	A	C	3640.03	.	AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;QD=28.53;SOR=0.761	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0
-20	10004725	.	A	G	972.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.217e+00;ClippingRankSum=-5.460e-01;DP=65;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.27;MQRankSum=2.07;QD=14.96;ReadPosRankSum=1.76;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168
+20	9999996	.	A	ACT	3799.03	.	AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.44;QD=25.36;SOR=1.075	GT:AD:DP:GQ:PL	1/1:0,84:84:99:3813,256,0
+20	10000117	.	C	T	926.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=-2.551e+00;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-2.370e-01;QD=14.48;ReadPosRankSum=1.01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
+20	10000211	.	C	T	962.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.84;ClippingRankSum=-1.201e+00;DP=54;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-5.600e-01;QD=18.16;ReadPosRankSum=1.72;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
+20	10000439	.	T	G	2819.06	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=28.73;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0
+20	10000598	.	T	A	1956.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=30.97;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0
+20	10000694	.	G	A	1029.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.57;ClippingRankSum=0.093;DP=82;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.66;MQRankSum=-4.109e+00;QD=12.56;ReadPosRankSum=1.14;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601
+20	10000758	.	T	A	3853.06	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=27.24;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0
+20	10001019	.	T	G	671.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.069e+00;ClippingRankSum=0.408;DP=65;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=49.49;MQRankSum=-6.448e+00;QD=10.33;ReadPosRankSum=-6.900e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426
+20	10001298	.	T	A	2932.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=28.20;SOR=0.963	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0
+20	10001436	.	A	AAGGCT	2325.03	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.88;QD=25.00;SOR=3.442	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2339,156,0
+20	10001474	.	C	T	2655.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;QD=29.56;SOR=1.516	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0
+20	10001617	.	C	A	1752.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.15;ClippingRankSum=-4.120e-01;DP=103;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-2.140e-01;QD=17.02;ReadPosRankSum=0.557;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781
+20	10001628	.	G	A	3913.06	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=30.62;SOR=1.053	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0
+20	10001661	.	T	C	3621.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=28.17;SOR=1.193	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0
+20	10001670	.	T	G	3688.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=26.80;SOR=0.995	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0
+20	10002058	.	T	G	2978.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.69;ClippingRankSum=0.577;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;MQRankSum=1.41;QD=26.00;ReadPosRankSum=0.762;SOR=0.776	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0
+20	10002099	.	C	T	1215.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;ClippingRankSum=0.020;DP=66;ExcessHet=3.0103;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-8.590e-01;QD=18.70;ReadPosRankSum=-3.660e-01;SOR=0.375	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844
+20	10002138	.	C	G	2458.06	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.38;QD=30.02;SOR=0.730	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0
+20	10002142	.	G	C	2422.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.31;QD=31.98;SOR=0.853	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,52:52:99:1|1:10002138_C_G:2436,166,0
+20	10002458	.	G	GTTT	2154.96	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.07;QD=27.51;SOR=2.049	GT:AD:DP:GQ:PL	1/1:0,6:16:99:2090,167,0
+20	10002470	.	C	T	2537.06	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;QD=29.11;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2551,189,0
+20	10002625	.	G	T	2680.06	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=28.08;SOR=1.127	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0
+20	10003021	.	C	T	2398.06	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;QD=23.23;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0
+20	10003358	.	A	C	1475.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;ClippingRankSum=0.513;DP=90;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=-3.700e-02;QD=16.58;ReadPosRankSum=0.078;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477
+20	10003651	.	T	C	3635.06	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=29.03;SOR=1.511	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0
+20	10003692	.	A	G	2624.06	.	AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=30.67;SOR=1.352	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0
+20	10003832	.	G	A	2720.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;QD=26.61;SOR=1.473	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0
+20	10004094	.	A	C	1840.06	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;QD=34.72;SOR=1.524	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0
+20	10004147	.	A	G	1852.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;QD=29.20;SOR=1.136	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0
+20	10004193	.	G	T	939.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.000e-01;ClippingRankSum=-1.110e-01;DP=53;ExcessHet=3.0103;FS=2.391;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=3.46;QD=18.07;ReadPosRankSum=0.737;SOR=1.019	GT:AD:DP:GQ:PL	0/1:23,29:52:99:947,0,775
+20	10004222	.	C	CA	42.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.157;ClippingRankSum=0.122;DP=55;ExcessHet=3.0103;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.05;MQRankSum=-2.139e+00;QD=1.09;ReadPosRankSum=-5.200e-02;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,8:39:50:50,0,923
+20	10004223	.	A	AG	77.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.650e-01;ClippingRankSum=0.289;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQRankSum=1.50;QD=1.65;ReadPosRankSum=2.12;SOR=0.638	GT:AD:DP:GQ:PL	0/1:36,11:47:85:85,0,982
+20	10004351	.	C	G	2770.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=28.55;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2784,211,0
+20	10004389	.	T	G	2509.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;QD=34.42;SOR=1.143	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0
+20	10004610	.	A	C	3640.06	.	AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;QD=28.53;SOR=0.761	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0
+20	10004725	.	A	G	972.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.217e+00;ClippingRankSum=-5.460e-01;DP=65;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.27;MQRankSum=2.07;QD=14.96;ReadPosRankSum=1.76;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168
 20	10004769	.	TAAAACTATGC	T	1011.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=-5.030e-01;DP=79;ExcessHet=3.0103;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.37;MQRankSum=-5.791e+00;QD=15.81;ReadPosRankSum=2.15;SOR=1.306	GT:AD:DP:GQ:PL	0/1:37,27:64:99:1019,0,1471
-20	10004874	.	A	C	3617.03	.	AC=2;AF=1.00;AN=2;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=27.23;SOR=1.286	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0
-20	10004887	.	A	G	1344.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;ClippingRankSum=0.357;DP=87;ExcessHet=3.0103;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.20;MQRankSum=0.427;QD=15.82;ReadPosRankSum=-4.000e-02;SOR=0.984	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,40:85:99:0|1:10004874_A_C:1352,0,1542
-20	10005010	.	C	T	2949.03	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=29.52;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2963,217,0
-20	10005427	.	C	T	2229.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;QD=33.47;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2243,165,0
-20	10005499	.	A	G	3068.03	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.91;SOR=1.121	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3082,229,0
-20	10005587	.	A	G	1250.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;ClippingRankSum=1.65;DP=73;ExcessHet=3.0103;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-8.500e-01;QD=17.37;ReadPosRankSum=1.36;SOR=0.848	GT:AD:DP:GQ:PL	0/1:36,36:72:99:1258,0,1236
-20	10005723	.	A	G	3077.03	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=31.31;SOR=0.947	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3091,258,0
-20	10006291	.	G	A	999.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;ClippingRankSum=0.093;DP=84;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.300e-01;QD=11.90;ReadPosRankSum=-1.390e-01;SOR=0.659	GT:AD:DP:GQ:PL	0/1:53,31:84:99:1007,0,1905
-20	10006404	.	A	C	2943.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.16;QD=31.45;SOR=1.432	GT:AD:DP:GQ:PL	1/1:0,76:76:99:2957,228,0
-20	10006682	.	T	A	2889.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=33.27;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2903,219,0
+20	10004874	.	A	C	3617.06	.	AC=2;AF=1.00;AN=2;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=27.23;SOR=1.286	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0
+20	10004887	.	A	G	1344.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;ClippingRankSum=0.357;DP=87;ExcessHet=3.0103;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.20;MQRankSum=0.427;QD=15.82;ReadPosRankSum=-4.000e-02;SOR=0.984	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,40:85:99:0|1:10004874_A_C:1352,0,1542
+20	10005010	.	C	T	2949.06	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=29.52;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2963,217,0
+20	10005427	.	C	T	2229.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;QD=33.47;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2243,165,0
+20	10005499	.	A	G	3068.06	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.91;SOR=1.121	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3082,229,0
+20	10005587	.	A	G	1250.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;ClippingRankSum=1.65;DP=73;ExcessHet=3.0103;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-8.500e-01;QD=17.37;ReadPosRankSum=1.36;SOR=0.848	GT:AD:DP:GQ:PL	0/1:36,36:72:99:1258,0,1236
+20	10005723	.	A	G	3077.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=31.31;SOR=0.947	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3091,258,0
+20	10006291	.	G	A	999.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;ClippingRankSum=0.093;DP=84;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.300e-01;QD=11.90;ReadPosRankSum=-1.390e-01;SOR=0.659	GT:AD:DP:GQ:PL	0/1:53,31:84:99:1007,0,1905
+20	10006404	.	A	C	2943.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.16;QD=31.45;SOR=1.432	GT:AD:DP:GQ:PL	1/1:0,76:76:99:2957,228,0
+20	10006682	.	T	A	2889.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=33.27;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2903,219,0
 20	10006819	.	AAAAC	A	2555.03	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.13;QD=31.26;SOR=0.762	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2569,176,0
-20	10007150	.	G	C	690.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.376e+00;ClippingRankSum=1.05;DP=63;ExcessHet=3.0103;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.550e-01;QD=10.96;ReadPosRankSum=-1.932e+00;SOR=0.746	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479
-20	10007175	.	C	T	1371.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.19;ClippingRankSum=0.275;DP=61;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=-3.940e-01;QD=22.49;ReadPosRankSum=-9.450e-01;SOR=0.434	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780
-20	10007352	.	C	T	2779.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=27.76;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0
-20	10007531	.	A	G	2935.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;QD=29.09;SOR=1.577	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2949,217,0
-20	10007980	.	A	C	3539.03	.	AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;QD=26.08;SOR=0.990	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0
-20	10008029	.	T	TA	2010.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.365;ClippingRankSum=0.338;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.98;MQRankSum=0.635;QD=26.80;ReadPosRankSum=-1.068e+00;SOR=0.788	GT:AD:DP:GQ:PL	1/1:3,72:75:99:2024,145,0
+20	10007150	.	G	C	690.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.376e+00;ClippingRankSum=1.05;DP=63;ExcessHet=3.0103;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.550e-01;QD=10.96;ReadPosRankSum=-1.932e+00;SOR=0.746	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479
+20	10007175	.	C	T	1371.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.19;ClippingRankSum=0.275;DP=61;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=-3.940e-01;QD=22.49;ReadPosRankSum=-9.450e-01;SOR=0.434	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780
+20	10007352	.	C	T	2779.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=27.76;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0
+20	10007531	.	A	G	2935.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;QD=29.09;SOR=1.577	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2949,217,0
+20	10007980	.	A	C	3539.06	.	AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;QD=26.08;SOR=0.990	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0
+20	10008029	.	T	TA	2010.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.365;ClippingRankSum=0.338;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.98;MQRankSum=0.635;QD=26.80;ReadPosRankSum=-1.068e+00;SOR=0.788	GT:AD:DP:GQ:PL	1/1:3,72:75:99:2024,145,0
 20	10008146	.	TA	T	2165.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.59;QD=30.93;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2179,211,0
-20	10008221	.	T	C	3239.03	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=33.85;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0
-20	10008458	.	T	G	2669.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.54;QD=27.08;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0
-20	10008742	.	G	T	736.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.96;ClippingRankSum=1.45;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.753e+00;QD=15.03;ReadPosRankSum=0.711;SOR=0.741	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580
-20	10008758	.	C	CA	707.53	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;ClippingRankSum=0.389;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-1.685e+00;QD=20.22;ReadPosRankSum=-3.890e-01;SOR=0.249	GT:AD:DP:GQ:PL	1/1:4,31:35:10:721,10,0
-20	10008921	.	C	CA	283.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;ClippingRankSum=1.12;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.259e+00;QD=8.34;ReadPosRankSum=-4.310e-01;SOR=0.512	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:34:99:0|1:10008921_C_CA:291,0,366
+20	10008221	.	T	C	3239.06	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=33.85;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0
+20	10008458	.	T	G	2669.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.54;QD=27.08;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0
+20	10008742	.	G	T	736.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.96;ClippingRankSum=1.45;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.753e+00;QD=15.03;ReadPosRankSum=0.711;SOR=0.741	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580
+20	10008758	.	C	CA	707.49	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;ClippingRankSum=0.389;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-1.685e+00;QD=20.21;ReadPosRankSum=-3.890e-01;SOR=0.249	GT:AD:DP:GQ:PL	1/1:4,31:35:10:721,10,0
+20	10008921	.	C	CA	283.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;ClippingRankSum=1.12;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.259e+00;QD=8.34;ReadPosRankSum=-4.310e-01;SOR=0.512	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:34:99:0|1:10008921_C_CA:291,0,366
 20	10008948	.	TA	T	2081.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.917;ClippingRankSum=1.26;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.30;MQRankSum=1.66;QD=25.42;ReadPosRankSum=0.713;SOR=0.818	GT:AD:DP:GQ:PGT:PID:PL	1/1:1,50:51:99:1|1:10008921_C_CA:2095,107,0
-20	10008952	.	CACACACACACA	C,CCACACACACA	1687.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.815;ClippingRankSum=-2.040e-01;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.81;MQRankSum=1.53;QD=27.65;ReadPosRankSum=0.612;SOR=1.127	GT:AD:DP:GQ:PL	1/2:1,14,11:34:99:1704,525,845,582,0,530
-20	10009227	.	A	G	1390.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.011e+00;ClippingRankSum=-1.574e+00;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.57;QD=22.43;ReadPosRankSum=0.262;SOR=0.281	GT:AD:DP:GQ:PL	0/1:23,39:62:99:1398,0,740
-20	10009246	.	A	G	3017.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=29.48;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3031,231,0
-20	10009400	.	T	A	3013.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.56;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0
-20	10009512	.	C	G	3054.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.47;QD=33.63;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3068,231,0
-20	10009719	.	A	G	1910.03	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.29;QD=32.37;SOR=0.950	GT:AD:DP:GQ:PL	1/1:0,59:59:99:1924,175,0
-20	10009795	.	A	G	1895.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=30.55;SOR=1.514	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1909,141,0
-20	10009842	.	G	GAA	562.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.832;ClippingRankSum=-8.320e-01;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQRankSum=-5.550e-01;QD=16.55;ReadPosRankSum=0.069;SOR=0.738	GT:AD:DP:GQ:PL	0/1:19,15:34:99:570,0,690
-20	10009844	.	G	A	682.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.745;ClippingRankSum=1.18;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=0.944;QD=19.50;ReadPosRankSum=0.348;SOR=0.793	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,19:35:99:0|1:10009844_G_A:690,0,586
-20	10009871	.	A	G	679.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.920e-01;ClippingRankSum=-3.170e-01;DP=61;ExcessHet=3.0103;FS=2.798;MLEAC=1;MLEAF=0.500;MQ=50.95;MQRankSum=1.11;QD=18.88;ReadPosRankSum=1.65;SOR=0.553	GT:AD:DP:GQ:PGT:PID:PL	0/1:17,19:36:99:0|1:10009844_G_A:687,0,594
+20	10008952	.	CACACACACACA	C,CCACACACACA	1687.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.815;ClippingRankSum=-2.040e-01;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.81;MQRankSum=1.53;QD=27.65;ReadPosRankSum=0.612;SOR=1.127	GT:AD:DP:GQ:PL	1/2:1,14,11:34:99:1704,525,845,582,0,530
+20	10009227	.	A	G	1390.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.011e+00;ClippingRankSum=-1.574e+00;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.57;QD=22.43;ReadPosRankSum=0.262;SOR=0.281	GT:AD:DP:GQ:PL	0/1:23,39:62:99:1398,0,740
+20	10009246	.	A	G	3017.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=29.48;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3031,231,0
+20	10009400	.	T	A	3013.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.56;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0
+20	10009512	.	C	G	3054.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.47;QD=33.63;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3068,231,0
+20	10009719	.	A	G	1910.06	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.29;QD=32.37;SOR=0.950	GT:AD:DP:GQ:PL	1/1:0,59:59:99:1924,175,0
+20	10009795	.	A	G	1895.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=30.55;SOR=1.514	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1909,141,0
+20	10009842	.	G	GAA	562.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.832;ClippingRankSum=-8.320e-01;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQRankSum=-5.550e-01;QD=16.55;ReadPosRankSum=0.069;SOR=0.738	GT:AD:DP:GQ:PL	0/1:19,15:34:99:570,0,690
+20	10009844	.	G	A	682.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.745;ClippingRankSum=1.18;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=0.944;QD=19.50;ReadPosRankSum=0.348;SOR=0.793	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,19:35:99:0|1:10009844_G_A:690,0,586
+20	10009871	.	A	G	679.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.920e-01;ClippingRankSum=-3.170e-01;DP=61;ExcessHet=3.0103;FS=2.798;MLEAC=1;MLEAF=0.500;MQ=50.95;MQRankSum=1.11;QD=18.88;ReadPosRankSum=1.65;SOR=0.553	GT:AD:DP:GQ:PGT:PID:PL	0/1:17,19:36:99:0|1:10009844_G_A:687,0,594
 20	10009875	.	A	G,AGGGAGG	2390.06	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.208;ClippingRankSum=1.46;DP=58;ExcessHet=3.0103;FS=6.794;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.04;QD=32.62;ReadPosRankSum=-1.250e-01;SOR=0.599	GT:AD:DP:GQ:PL	1/2:2,15,13:30:99:2407,645,533,697,0,574
-20	10009879	.	A	G	2259.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.328;DP=50;ExcessHet=3.0103;FS=9.369;MLEAC=2;MLEAF=1.00;MQ=49.85;MQRankSum=0.884;QD=29.33;ReadPosRankSum=1.24;SOR=1.474	GT:AD:DP:GQ:PL	1/1:2,47:49:99:2273,150,0
-20	10009883	.	A	G	2166.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.56;QD=35.36;SOR=1.659	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2180,147,0
-20	10010393	.	T	G	1485.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.495e+00;ClippingRankSum=-8.910e-01;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.363e+00;QD=18.81;ReadPosRankSum=-1.363e+00;SOR=0.606	GT:AD:DP:GQ:PL	0/1:36,43:79:99:1493,0,1230
-20	10010536	.	G	GA	2486.06	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.63;QD=31.47;SOR=0.881	GT:AD:DP:GQ:PL	1/1:0,79:79:99:2500,243,0
-20	10010766	.	T	G	2426.03	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.30;SOR=0.818	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2440,199,0
-20	10010832	.	T	C	2966.03	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;QD=27.00;SOR=1.091	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2980,226,0
-20	10011075	.	C	T	1346.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.46;ClippingRankSum=-4.060e-01;DP=85;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.430e-01;QD=16.22;ReadPosRankSum=-5.160e-01;SOR=0.968	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1354,0,1333
-20	10011309	.	T	C	2707.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.82;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2721,231,0
-20	10011517	.	GA	G	520.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.965;ClippingRankSum=-3.030e-01;DP=91;ExcessHet=3.0103;FS=3.171;MLEAC=1;MLEAF=0.500;MQ=59.90;MQRankSum=-6.340e-01;QD=8.01;ReadPosRankSum=1.15;SOR=0.394	GT:AD:DP:GQ:PL	0/1:37,28:73:99:528,0,875
-20	10011666	.	C	T	2976.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.27;SOR=1.103	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2990,220,0
-20	10011939	.	C	T	2484.03	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.26;QD=35.92;SOR=1.292	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2498,184,0
+20	10009879	.	A	G	2259.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.328;DP=50;ExcessHet=3.0103;FS=9.369;MLEAC=2;MLEAF=1.00;MQ=49.85;MQRankSum=0.884;QD=29.33;ReadPosRankSum=1.24;SOR=1.474	GT:AD:DP:GQ:PL	1/1:2,47:49:99:2273,150,0
+20	10009883	.	A	G	2166.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.56;QD=35.36;SOR=1.659	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2180,147,0
+20	10010393	.	T	G	1485.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.495e+00;ClippingRankSum=-8.910e-01;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.363e+00;QD=18.81;ReadPosRankSum=-1.363e+00;SOR=0.606	GT:AD:DP:GQ:PL	0/1:36,43:79:99:1493,0,1230
+20	10010536	.	G	GA	2486.03	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.63;QD=31.47;SOR=0.881	GT:AD:DP:GQ:PL	1/1:0,79:79:99:2500,243,0
+20	10010766	.	T	G	2426.06	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.30;SOR=0.818	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2440,199,0
+20	10010832	.	T	C	2966.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;QD=27.00;SOR=1.091	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2980,226,0
+20	10011075	.	C	T	1346.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.46;ClippingRankSum=-4.060e-01;DP=85;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.430e-01;QD=16.22;ReadPosRankSum=-5.160e-01;SOR=0.968	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1354,0,1333
+20	10011309	.	T	C	2707.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.82;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2721,231,0
+20	10011517	.	GA	G	520.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.965;ClippingRankSum=-3.030e-01;DP=91;ExcessHet=3.0103;FS=3.171;MLEAC=1;MLEAF=0.500;MQ=59.90;MQRankSum=-6.340e-01;QD=8.01;ReadPosRankSum=1.15;SOR=0.394	GT:AD:DP:GQ:PL	0/1:37,28:73:99:528,0,875
+20	10011666	.	C	T	2976.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.27;SOR=1.103	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2990,220,0
+20	10011939	.	C	T	2484.06	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.26;QD=35.92;SOR=1.292	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2498,184,0
 20	10012021	.	CA	C	1999.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;QD=30.29;SOR=1.196	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2013,198,0
-20	10012362	.	G	T	850.03	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.78;QD=29.63;SOR=4.003	GT:AD:DP:GQ:PL	1/1:0,23:23:69:864,69,0
-20	10012384	.	T	C	250.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.733e+00;ClippingRankSum=-1.644e+00;DP=19;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.500;MQ=53.75;MQRankSum=-4.890e-01;QD=13.92;ReadPosRankSum=0.044;SOR=0.044	GT:AD:DP:GQ:PL	0/1:10,8:18:99:258,0,355
-20	10012387	.	T	C	548.03	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.96;QD=34.25;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,16:16:50:562,50,0
-20	10012479	.	A	G	607.03	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=28.76;SOR=0.804	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,17:17:50:1|1:10012479_A_G:621,50,0
-20	10012498	.	C	G	481.02	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;QD=29.94;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012479_A_G:495,33,0
-20	10012518	.	T	C	421.02	.	AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;QD=31.54;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:30:1|1:10012479_A_G:435,30,0
-20	10012521	.	C	T	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.77;MQRankSum=-7.150e-01;QD=6.15;ReadPosRankSum=1.93;SOR=1.179	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,224
-20	10012570	.	G	GCA	481.06	.	AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.55;QD=28.86;SOR=3.056	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0
+20	10012362	.	G	T	850.06	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.78;QD=29.63;SOR=4.003	GT:AD:DP:GQ:PL	1/1:0,23:23:69:864,69,0
+20	10012384	.	T	C	250.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.733e+00;ClippingRankSum=-1.644e+00;DP=19;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.500;MQ=53.75;MQRankSum=-4.890e-01;QD=13.92;ReadPosRankSum=0.044;SOR=0.044	GT:AD:DP:GQ:PL	0/1:10,8:18:99:258,0,355
+20	10012387	.	T	C	548.06	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.96;QD=34.25;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,16:16:50:562,50,0
+20	10012479	.	A	G	607.06	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=28.76;SOR=0.804	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,17:17:50:1|1:10012479_A_G:621,50,0
+20	10012498	.	C	G	481.06	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;QD=29.94;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012479_A_G:495,33,0
+20	10012518	.	T	C	421.06	.	AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;QD=31.54;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:30:1|1:10012479_A_G:435,30,0
+20	10012521	.	C	T	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.77;MQRankSum=-7.150e-01;QD=6.15;ReadPosRankSum=1.93;SOR=1.179	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,224
+20	10012570	.	G	GCA	481.02	.	AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.55;QD=28.86;SOR=3.056	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0
 20	10012572	.	GT	G	481.02	.	AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.52;QD=29.41;SOR=3.442	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012570_G_GCA:495,33,0
-20	10012631	.	C	CG	514.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.050e+00;ClippingRankSum=-6.160e-01;DP=22;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=47.53;MQRankSum=-1.485e+00;QD=24.51;ReadPosRankSum=-8.330e-01;SOR=0.048	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297
-20	10012636	.	G	C	548.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=-8.530e-01;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-6.480e-01;QD=24.94;ReadPosRankSum=-7.170e-01;SOR=0.058	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,14:22:99:0|1:10012631_C_CG:556,0,294
-20	10012714	.	G	C	1315.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.04;QD=31.11;SOR=2.964	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1329,105,0
-20	10012751	.	T	C	952.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.56;QD=31.73;SOR=0.976	GT:AD:DP:GQ:PL	1/1:0,30:30:89:966,89,0
-20	10013119	.	C	T	1032.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;ClippingRankSum=-9.320e-01;DP=59;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.48;MQRankSum=-5.380e-01;QD=17.50;ReadPosRankSum=1.13;SOR=0.405	GT:AD:DP:GQ:PL	0/1:29,30:59:99:1040,0,936
-20	10013574	.	G	A	1071.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.68;ClippingRankSum=-1.800e-02;DP=70;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.09;MQRankSum=0.597;QD=15.53;ReadPosRankSum=0.826;SOR=1.675	GT:AD:DP:GQ:PL	0/1:38,31:69:99:1079,0,1301
-20	10014990	.	C	CAT	1267.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.127e+00;DP=87;ExcessHet=3.0103;FS=2.090;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=0.442;QD=16.68;ReadPosRankSum=-3.690e-01;SOR=0.403	GT:AD:DP:GQ:PL	0/1:38,38:76:99:1275,0,1248
-20	10015679	.	C	T	161.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.336;ClippingRankSum=1.67;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.470;QD=16.16;ReadPosRankSum=0.851;SOR=0.693	GT:AD:DP:GQ:PL	0/1:5,5:10:99:169,0,166
-20	10015761	.	T	C	365.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.003e+00;ClippingRankSum=0.467;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQRankSum=-1.536e+00;QD=16.62;ReadPosRankSum=1.07;SOR=0.352	GT:AD:DP:GQ:PL	0/1:9,13:22:99:373,0,284
-20	10018158	.	G	C	1660.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.82;ClippingRankSum=0.155;DP=89;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=0.884;QD=18.87;ReadPosRankSum=0.918;SOR=0.834	GT:AD:DP:GQ:PL	0/1:40,48:88:99:1668,0,1165
-20	10018555	.	G	A	1588.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.980e-01;ClippingRankSum=0.398;DP=80;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.070e-01;QD=19.86;ReadPosRankSum=0.252;SOR=0.627	GT:AD:DP:GQ:PL	0/1:35,45:80:99:1596,0,1211
-20	10019093	.	A	G	1265.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;ClippingRankSum=1.82;DP=69;ExcessHet=3.0103;FS=1.990;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=-2.036e+00;QD=18.34;ReadPosRankSum=0.474;SOR=0.665	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1273,0,1104
-20	10020229	.	G	A	1559.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.71;ClippingRankSum=-3.770e-01;DP=82;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.302;QD=19.02;ReadPosRankSum=-3.860e-01;SOR=0.573	GT:AD:DP:GQ:PL	0/1:38,44:82:99:1567,0,1130
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-20	10024300	.	C	CTT	104.67	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;ClippingRankSum=0.00;DP=50;ExcessHet=3.0103;FS=6.107;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-1.303e+00;QD=9.52;ReadPosRankSum=0.063;SOR=1.825	GT:AD:DP:GQ:PL	0/1:3,8:18:99:103,0,137
-20	10026357	.	T	C	1187.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.279e+00;ClippingRankSum=-5.460e-01;DP=64;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.46;MQRankSum=-7.600e-02;QD=18.85;ReadPosRankSum=-1.450e-01;SOR=0.722	GT:AD:DP:GQ:PL	0/1:28,35:63:99:1195,0,932
-20	10026794	.	C	T	1105.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.87;ClippingRankSum=-6.460e-01;DP=54;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=1.54;QD=21.26;ReadPosRankSum=-3.040e-01;SOR=0.428	GT:AD:DP:GQ:PL	0/1:19,33:52:99:1113,0,529
-20	10027234	.	A	ATTAG	1350.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=0.582;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=0.270;QD=19.57;ReadPosRankSum=-8.820e-01;SOR=0.926	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1358,0,1964
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-20	10027872	.	A	G	1745.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.278e+00;ClippingRankSum=-9.110e-01;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.048;QD=20.54;ReadPosRankSum=1.05;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136
-20	10028867	.	A	ATG	1136.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.330e-01;ClippingRankSum=-1.705e+00;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=0.295;QD=16.01;ReadPosRankSum=0.075;SOR=0.336	GT:AD:DP:GQ:PL	0/1:32,39:71:99:1144,0,916
-20	10030188	.	T	A	1393.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;ClippingRankSum=0.969;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=2.05;QD=17.20;ReadPosRankSum=0.250;SOR=1.105	GT:AD:DP:GQ:PL	0/1:42,39:81:99:1401,0,1524
-20	10031254	.	A	AT	1493.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;ClippingRankSum=0.588;DP=88;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.429;QD=17.57;ReadPosRankSum=0.455;SOR=0.211	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1501,0,1159
-20	10031342	.	G	A	1855.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;ClippingRankSum=-3.440e-01;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-5.530e-01;QD=19.95;ReadPosRankSum=-2.440e-01;SOR=0.955	GT:AD:DP:GQ:PL	0/1:41,52:93:99:1863,0,1375
-20	10031798	.	G	A	4311.03	.	AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=34.66;SOR=0.900	GT:AD:DP:GQ:PL	1/1:0,104:104:99:4325,313,0
-20	10031827	.	C	T	2025.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.40;ClippingRankSum=0.858;DP=108;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=-5.560e-01;QD=18.76;ReadPosRankSum=0.526;SOR=0.382	GT:AD:DP:GQ:PL	0/1:52,56:108:99:2033,0,1798
-20	10032094	.	G	A	1241.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.43;ClippingRankSum=-1.610e-01;DP=84;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.510;QD=14.96;ReadPosRankSum=0.629;SOR=0.260	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1249,0,1497
-20	10032413	.	T	G	890.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.949e+00;ClippingRankSum=-5.520e-01;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=1.41;QD=13.49;ReadPosRankSum=-2.310e-01;SOR=1.293	GT:AD:DP:GQ:PL	0/1:35,31:66:99:898,0,1277
-20	10032882	.	A	T	1223.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.632e+00;ClippingRankSum=-8.960e-01;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.914e+00;QD=16.31;ReadPosRankSum=1.17;SOR=0.338	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1231,0,1406
-20	10032972	.	C	CAT	1152.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.680e-01;ClippingRankSum=-1.030e-01;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-2.236e+00;QD=18.30;ReadPosRankSum=-1.218e+00;SOR=1.300	GT:AD:DP:GQ:PL	0/1:33,30:63:99:1160,0,1477
-20	10034306	.	T	C	803.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.607e+00;ClippingRankSum=-4.080e-01;DP=77;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.125;QD=10.71;ReadPosRankSum=0.908;SOR=0.685	GT:AD:DP:GQ:PL	0/1:46,29:75:99:811,0,1593
+20	10012631	.	C	CG	514.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.050e+00;ClippingRankSum=-6.160e-01;DP=22;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=47.53;MQRankSum=-1.485e+00;QD=24.50;ReadPosRankSum=-8.330e-01;SOR=0.048	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297
+20	10012636	.	G	C	548.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=-8.530e-01;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-6.480e-01;QD=24.94;ReadPosRankSum=-7.170e-01;SOR=0.058	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,14:22:99:0|1:10012631_C_CG:556,0,294
+20	10012714	.	G	C	1315.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.04;QD=31.11;SOR=2.964	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1329,105,0
+20	10012751	.	T	C	952.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.56;QD=31.74;SOR=0.976	GT:AD:DP:GQ:PL	1/1:0,30:30:89:966,89,0
+20	10013119	.	C	T	1032.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;ClippingRankSum=-9.320e-01;DP=59;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.48;MQRankSum=-5.380e-01;QD=17.50;ReadPosRankSum=1.13;SOR=0.405	GT:AD:DP:GQ:PL	0/1:29,30:59:99:1040,0,936
+20	10013574	.	G	A	1071.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.68;ClippingRankSum=-1.800e-02;DP=70;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.09;MQRankSum=0.597;QD=15.53;ReadPosRankSum=0.826;SOR=1.675	GT:AD:DP:GQ:PL	0/1:38,31:69:99:1079,0,1301
+20	10014990	.	C	CAT	1267.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.127e+00;DP=87;ExcessHet=3.0103;FS=2.090;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=0.442;QD=16.68;ReadPosRankSum=-3.690e-01;SOR=0.403	GT:AD:DP:GQ:PL	0/1:38,38:76:99:1275,0,1248
+20	10015679	.	C	T	161.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.336;ClippingRankSum=1.67;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.470;QD=16.16;ReadPosRankSum=0.851;SOR=0.693	GT:AD:DP:GQ:PL	0/1:5,5:10:99:169,0,166
+20	10015761	.	T	C	365.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.003e+00;ClippingRankSum=0.467;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQRankSum=-1.536e+00;QD=16.62;ReadPosRankSum=1.07;SOR=0.352	GT:AD:DP:GQ:PL	0/1:9,13:22:99:373,0,284
+20	10018158	.	G	C	1660.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.82;ClippingRankSum=0.155;DP=89;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=0.884;QD=18.87;ReadPosRankSum=0.918;SOR=0.834	GT:AD:DP:GQ:PL	0/1:40,48:88:99:1668,0,1165
+20	10018555	.	G	A	1588.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.980e-01;ClippingRankSum=0.398;DP=80;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.070e-01;QD=19.86;ReadPosRankSum=0.252;SOR=0.627	GT:AD:DP:GQ:PL	0/1:35,45:80:99:1596,0,1211
+20	10019093	.	A	G	1265.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;ClippingRankSum=1.82;DP=69;ExcessHet=3.0103;FS=1.990;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=-2.036e+00;QD=18.34;ReadPosRankSum=0.474;SOR=0.665	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1273,0,1104
+20	10020229	.	G	A	1559.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.71;ClippingRankSum=-3.770e-01;DP=82;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.302;QD=19.02;ReadPosRankSum=-3.860e-01;SOR=0.573	GT:AD:DP:GQ:PL	0/1:38,44:82:99:1567,0,1130
+20	10023689	.	G	A	1873.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.88;ClippingRankSum=-1.900e-01;DP=80;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=-2.000e-02;QD=23.42;ReadPosRankSum=1.15;SOR=0.549	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1881,0,946
+20	10024107	.	C	T	1715.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.62;ClippingRankSum=-4.800e-02;DP=86;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=0.700;QD=19.95;ReadPosRankSum=1.11;SOR=0.823	GT:AD:DP:GQ:PL	0/1:38,48:86:99:1723,0,1086
+20	10024300	.	C	CTT	104.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;ClippingRankSum=0.00;DP=50;ExcessHet=3.0103;FS=6.107;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-1.303e+00;QD=9.51;ReadPosRankSum=0.063;SOR=1.825	GT:AD:DP:GQ:PL	0/1:3,8:18:99:103,0,137
+20	10026357	.	T	C	1187.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.279e+00;ClippingRankSum=-5.460e-01;DP=64;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.46;MQRankSum=-7.600e-02;QD=18.85;ReadPosRankSum=-1.450e-01;SOR=0.722	GT:AD:DP:GQ:PL	0/1:28,35:63:99:1195,0,932
+20	10026794	.	C	T	1105.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.87;ClippingRankSum=-6.460e-01;DP=54;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=1.54;QD=21.26;ReadPosRankSum=-3.040e-01;SOR=0.428	GT:AD:DP:GQ:PL	0/1:19,33:52:99:1113,0,529
+20	10027234	.	A	ATTAG	1350.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=0.582;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=0.270;QD=19.57;ReadPosRankSum=-8.820e-01;SOR=0.926	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1358,0,1964
+20	10027868	.	A	G	1760.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.601e+00;ClippingRankSum=-6.280e-01;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=1.11;QD=19.78;ReadPosRankSum=1.11;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,45:89:99:0|1:10027868_A_G:1768,0,3201
+20	10027872	.	A	G	1745.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.278e+00;ClippingRankSum=-9.110e-01;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.048;QD=20.54;ReadPosRankSum=1.05;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136
+20	10028867	.	A	ATG	1136.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.330e-01;ClippingRankSum=-1.705e+00;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=0.295;QD=16.01;ReadPosRankSum=0.075;SOR=0.336	GT:AD:DP:GQ:PL	0/1:32,39:71:99:1144,0,916
+20	10030188	.	T	A	1393.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;ClippingRankSum=0.969;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=2.05;QD=17.21;ReadPosRankSum=0.250;SOR=1.105	GT:AD:DP:GQ:PL	0/1:42,39:81:99:1401,0,1524
+20	10031254	.	A	AT	1493.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;ClippingRankSum=0.588;DP=88;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.429;QD=17.57;ReadPosRankSum=0.455;SOR=0.211	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1501,0,1159
+20	10031342	.	G	A	1855.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;ClippingRankSum=-3.440e-01;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-5.530e-01;QD=19.95;ReadPosRankSum=-2.440e-01;SOR=0.955	GT:AD:DP:GQ:PL	0/1:41,52:93:99:1863,0,1375
+20	10031798	.	G	A	4311.06	.	AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=34.66;SOR=0.900	GT:AD:DP:GQ:PL	1/1:0,104:104:99:4325,313,0
+20	10031827	.	C	T	2025.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.40;ClippingRankSum=0.858;DP=108;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=-5.560e-01;QD=18.76;ReadPosRankSum=0.526;SOR=0.382	GT:AD:DP:GQ:PL	0/1:52,56:108:99:2033,0,1798
+20	10032094	.	G	A	1241.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.43;ClippingRankSum=-1.610e-01;DP=84;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.510;QD=14.96;ReadPosRankSum=0.629;SOR=0.260	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1249,0,1497
+20	10032413	.	T	G	890.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.949e+00;ClippingRankSum=-5.520e-01;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=1.41;QD=13.49;ReadPosRankSum=-2.310e-01;SOR=1.293	GT:AD:DP:GQ:PL	0/1:35,31:66:99:898,0,1277
+20	10032882	.	A	T	1223.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.632e+00;ClippingRankSum=-8.960e-01;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.914e+00;QD=16.32;ReadPosRankSum=1.17;SOR=0.338	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1231,0,1406
+20	10032972	.	C	CAT	1152.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.680e-01;ClippingRankSum=-1.030e-01;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-2.236e+00;QD=18.30;ReadPosRankSum=-1.218e+00;SOR=1.300	GT:AD:DP:GQ:PL	0/1:33,30:63:99:1160,0,1477
+20	10034306	.	T	C	803.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.607e+00;ClippingRankSum=-4.080e-01;DP=77;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.125;QD=10.72;ReadPosRankSum=0.908;SOR=0.685	GT:AD:DP:GQ:PL	0/1:46,29:75:99:811,0,1593
 20	10036930	.	CGATAGCCCTAGCCCTAGATA	C	1066.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.260;ClippingRankSum=0.980;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-3.633e+00;QD=15.69;ReadPosRankSum=0.139;SOR=0.269	GT:AD:DP:GQ:PL	0/1:39,29:68:99:1074,0,5571
-20	10037037	.	C	T	1457.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.29;ClippingRankSum=-1.560e-01;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-2.400e-02;QD=18.00;ReadPosRankSum=-1.734e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:39,42:81:99:1465,0,1124
-20	10037110	.	T	TGATA	2804.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=29.40;SOR=1.022	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2818,189,0
-20	10037144	.	T	TGATAGATA	1847.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=36.76;SOR=1.061	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1861,127,0
-20	10037709	.	A	T	1024.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.768e+00;ClippingRankSum=-3.060e-01;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=-3.180e-01;QD=14.43;ReadPosRankSum=1.35;SOR=0.608	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1032,0,1354
-20	10039371	.	T	G	1345.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.227e+00;ClippingRankSum=-1.209e+00;DP=74;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.170e-01;QD=18.18;ReadPosRankSum=1.28;SOR=1.031	GT:AD:DP:GQ:PL	0/1:34,40:74:99:1353,0,1194
-20	10040772	.	C	CT	2019.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.69;QD=28.84;SOR=0.811	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2033,210,0
+20	10037037	.	C	T	1457.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.29;ClippingRankSum=-1.560e-01;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-2.400e-02;QD=18.00;ReadPosRankSum=-1.734e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:39,42:81:99:1465,0,1124
+20	10037110	.	T	TGATA	2804.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=29.40;SOR=1.022	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2818,189,0
+20	10037144	.	T	TGATAGATA	1847.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=36.76;SOR=1.061	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1861,127,0
+20	10037709	.	A	T	1024.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.768e+00;ClippingRankSum=-3.060e-01;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=-3.180e-01;QD=14.43;ReadPosRankSum=1.35;SOR=0.608	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1032,0,1354
+20	10039371	.	T	G	1345.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.227e+00;ClippingRankSum=-1.209e+00;DP=74;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.170e-01;QD=18.18;ReadPosRankSum=1.28;SOR=1.031	GT:AD:DP:GQ:PL	0/1:34,40:74:99:1353,0,1194
+20	10040772	.	C	CT	2019.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.69;QD=28.84;SOR=0.811	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2033,210,0
 20	10040812	.	AT	A	2631.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;QD=30.54;SOR=0.721	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2645,214,0
-20	10040821	.	T	A	1192.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.850e-01;ClippingRankSum=-2.050e-01;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=0.415;QD=15.29;ReadPosRankSum=-1.435e+00;SOR=0.688	GT:AD:DP:GQ:PL	0/1:38,40:78:99:1200,0,1099
-20	10041304	.	C	T	2780.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.40;QD=21.53;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2794,204,0
-20	10041701	.	A	ATATG	1433.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.714;ClippingRankSum=-3.860e-01;DP=78;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.90;MQRankSum=1.30;QD=25.60;ReadPosRankSum=0.386;SOR=0.260	GT:AD:DP:GQ:PL	0/1:8,48:56:58:1441,0,58
-20	10042319	.	C	T	2673.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=34.87;SOR=1.033	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2687,199,0
-20	10042761	.	A	G	3568.03	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.04;SOR=1.389	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3582,272,0
-20	10042829	.	A	G	3070.03	.	AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;QD=27.86;SOR=0.855	GT:AD:DP:GQ:PL	1/1:0,78:78:99:3084,235,0
-20	10043002	.	A	T	1308.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.90;ClippingRankSum=-6.830e-01;DP=87;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-6.390e-01;QD=15.22;ReadPosRankSum=0.630;SOR=0.434	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1316,0,1659
-20	10044849	.	A	G	2106.03	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=34.17;SOR=1.316	GT:AD:DP:GQ:PL	1/1:0,59:59:99:2120,177,0
-20	10045078	.	G	T	3286.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;QD=28.60;SOR=0.876	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3300,244,0
-20	10045642	.	G	C	3122.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=25.57;SOR=0.821	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3136,243,0
+20	10040821	.	T	A	1192.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.850e-01;ClippingRankSum=-2.050e-01;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=0.415;QD=15.29;ReadPosRankSum=-1.435e+00;SOR=0.688	GT:AD:DP:GQ:PL	0/1:38,40:78:99:1200,0,1099
+20	10041304	.	C	T	2780.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.40;QD=21.53;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2794,204,0
+20	10041701	.	A	ATATG	1433.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.714;ClippingRankSum=-3.860e-01;DP=78;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.90;MQRankSum=1.30;QD=25.60;ReadPosRankSum=0.386;SOR=0.260	GT:AD:DP:GQ:PL	0/1:8,48:56:58:1441,0,58
+20	10042319	.	C	T	2673.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=34.87;SOR=1.033	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2687,199,0
+20	10042761	.	A	G	3568.06	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.04;SOR=1.389	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3582,272,0
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+20	10043002	.	A	T	1308.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.90;ClippingRankSum=-6.830e-01;DP=87;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-6.390e-01;QD=15.22;ReadPosRankSum=0.630;SOR=0.434	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1316,0,1659
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 20	10046178	.	AAGAAAGAAAG	A	2183.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.22;QD=33.11;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2197,152,0
-20	10046537	.	A	G	840.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.903e+00;ClippingRankSum=0.503;DP=57;ExcessHet=3.0103;FS=3.724;MLEAC=1;MLEAF=0.500;MQ=54.50;MQRankSum=-1.365e+00;QD=14.75;ReadPosRankSum=1.62;SOR=1.262	GT:AD:DP:GQ:PL	0/1:28,29:57:99:848,0,902
-20	10050828	.	T	C	1248.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-4.880e-01;DP=87;ExcessHet=3.0103;FS=2.887;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=-4.010e-01;QD=14.52;ReadPosRankSum=1.28;SOR=0.521	GT:AD:DP:GQ:PL	0/1:49,37:86:99:1256,0,1768
-20	10051448	.	T	C	1155.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.460e-01;ClippingRankSum=-1.316e+00;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=0.634;QD=16.51;ReadPosRankSum=1.07;SOR=0.302	GT:AD:DP:GQ:PL	0/1:35,35:70:99:1163,0,1150
-20	10052688	.	C	A	1083.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;ClippingRankSum=-1.308e+00;DP=77;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=-9.800e-02;QD=14.07;ReadPosRankSum=1.94;SOR=0.379	GT:AD:DP:GQ:PL	0/1:45,32:77:99:1091,0,1645
-20	10058022	.	T	C	996.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.861e+00;ClippingRankSum=0.510;DP=68;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=-3.100e-02;QD=14.66;ReadPosRankSum=0.522;SOR=0.849	GT:AD:DP:GQ:PL	0/1:36,32:68:99:1004,0,1261
-20	10062935	.	C	CA	122.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.45;ClippingRankSum=-1.453e+00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.23;MQRankSum=-6.340e-01;QD=8.18;ReadPosRankSum=-5.910e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:5,10:23:99:130,0,101
-20	10067049	.	TAAAAAAAA	T,TA	634.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.057;ClippingRankSum=0.628;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.41;MQRankSum=0.400;QD=30.20;ReadPosRankSum=-5.780e-01;SOR=1.127	GT:AD:DP:GQ:PL	1/2:2,7,9:22:99:651,164,340,135,0,106
-20	10067090	.	C	A	2019.03	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=30.49;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2033,164,0
-20	10067264	.	G	A	2937.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=31.67;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0
-20	10067722	.	A	C	2161.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.53;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
+20	10046537	.	A	G	840.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.903e+00;ClippingRankSum=0.503;DP=57;ExcessHet=3.0103;FS=3.724;MLEAC=1;MLEAF=0.500;MQ=54.50;MQRankSum=-1.365e+00;QD=14.75;ReadPosRankSum=1.62;SOR=1.262	GT:AD:DP:GQ:PL	0/1:28,29:57:99:848,0,902
+20	10050828	.	T	C	1248.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-4.880e-01;DP=87;ExcessHet=3.0103;FS=2.887;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=-4.010e-01;QD=14.52;ReadPosRankSum=1.28;SOR=0.521	GT:AD:DP:GQ:PL	0/1:49,37:86:99:1256,0,1768
+20	10051448	.	T	C	1155.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.460e-01;ClippingRankSum=-1.316e+00;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=0.634;QD=16.51;ReadPosRankSum=1.07;SOR=0.302	GT:AD:DP:GQ:PL	0/1:35,35:70:99:1163,0,1150
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+20	10058022	.	T	C	996.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.861e+00;ClippingRankSum=0.510;DP=68;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=-3.100e-02;QD=14.66;ReadPosRankSum=0.522;SOR=0.849	GT:AD:DP:GQ:PL	0/1:36,32:68:99:1004,0,1261
+20	10062935	.	C	CA	122.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.45;ClippingRankSum=-1.453e+00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.23;MQRankSum=-6.340e-01;QD=8.17;ReadPosRankSum=-5.910e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:5,10:23:99:130,0,101
+20	10067049	.	TAAAAAAAA	T,TA	634.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.057;ClippingRankSum=0.628;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.41;MQRankSum=0.400;QD=30.20;ReadPosRankSum=-5.780e-01;SOR=1.127	GT:AD:DP:GQ:PL	1/2:2,7,9:22:99:651,164,340,135,0,106
+20	10067090	.	C	A	2019.06	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=30.49;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2033,164,0
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 20	10068158	.	GTGTATATATATA	G	96.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-01;ClippingRankSum=0.937;DP=29;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=0.00;QD=13.80;ReadPosRankSum=-7.200e-01;SOR=0.061	GT:AD:DP:GQ:PGT:PID:PL	0/1:3,4:7:57:0|1:10068158_GTGTATATATATA_G:104,0,57
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-20	10068981	.	G	A	2518.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.63;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0
-20	10070602	.	T	C	2706.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.74;QD=30.36;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
-20	10070936	.	T	A	3646.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;QD=28.13;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10070936_T_A:3660,247,0
-20	10070938	.	G	GA	3680.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.10;QD=27.97;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,79:79:99:1|1:10070936_T_A:3694,250,0
-20	10071135	.	C	T	3272.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=28.31;SOR=1.003	GT:AD:DP:GQ:PL	1/1:0,79:79:99:3286,238,0
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-20	10071890	.	T	C	1989.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=34.90;SOR=0.728	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2003,171,0
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-20	10074240	.	T	C	3421.03	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=29.59;SOR=0.922	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3435,255,0
-20	10074716	.	G	A	2415.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;QD=32.25;SOR=1.214	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2429,192,0
-20	10074806	.	G	A	2832.03	.	AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=34.86;SOR=0.840	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2846,213,0
-20	10075043	.	T	C	2420.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.63;QD=32.49;SOR=1.107	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2434,184,0
-20	10075168	.	C	T	3627.03	.	AC=2;AF=1.00;AN=2;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=29.05;SOR=0.997	GT:AD:DP:GQ:PL	1/1:0,88:88:99:3641,264,0
+20	10068981	.	G	A	2518.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.63;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0
+20	10070602	.	T	C	2706.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.74;QD=30.36;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
+20	10070936	.	T	A	3646.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;QD=28.13;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10070936_T_A:3660,247,0
+20	10070938	.	G	GA	3680.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.10;QD=27.97;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,79:79:99:1|1:10070936_T_A:3694,250,0
+20	10071135	.	C	T	3272.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=28.31;SOR=1.003	GT:AD:DP:GQ:PL	1/1:0,79:79:99:3286,238,0
+20	10071187	.	G	A	3425.06	.	AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;QD=35.21;SOR=1.367	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3439,246,0
+20	10071890	.	T	C	1989.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=34.90;SOR=0.728	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2003,171,0
+20	10072505	.	A	G	2114.06	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.03;SOR=0.822	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2128,191,0
+20	10074187	.	A	G	3116.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=35.18;SOR=0.881	GT:AD:DP:GQ:PL	1/1:0,79:79:99:3130,238,0
+20	10074240	.	T	C	3421.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=29.59;SOR=0.922	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3435,255,0
+20	10074716	.	G	A	2415.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;QD=32.25;SOR=1.214	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2429,192,0
+20	10074806	.	G	A	2832.06	.	AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=34.86;SOR=0.840	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2846,213,0
+20	10075043	.	T	C	2420.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.63;QD=32.49;SOR=1.107	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2434,184,0
+20	10075168	.	C	T	3627.06	.	AC=2;AF=1.00;AN=2;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=29.05;SOR=0.997	GT:AD:DP:GQ:PL	1/1:0,88:88:99:3641,264,0
 20	10075508	.	GA	G	1952.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.17;QD=27.89;SOR=1.085	GT:AD:DP:GQ:PL	1/1:0,70:70:99:1966,210,0
-20	10076250	.	A	G	1128.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.319e+00;ClippingRankSum=0.260;DP=80;ExcessHet=3.0103;FS=7.546;MLEAC=1;MLEAF=0.500;MQ=59.40;MQRankSum=0.387;QD=14.29;ReadPosRankSum=-5.000e-03;SOR=0.344	GT:AD:DP:GQ:PL	0/1:40,39:79:99:1136,0,1339
-20	10076339	.	A	G	1330.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.028;ClippingRankSum=1.23;DP=72;ExcessHet=3.0103;FS=1.992;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=-1.700e-02;QD=18.48;ReadPosRankSum=0.833;SOR=0.446	GT:AD:DP:GQ:PL	0/1:32,40:72:99:1338,0,1035
-20	10076399	.	G	A	1828.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.85;ClippingRankSum=0.974;DP=94;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.959;QD=19.45;ReadPosRankSum=-7.990e-01;SOR=0.952	GT:AD:DP:GQ:PL	0/1:44,50:94:99:1836,0,1544
-20	10076989	.	CA	C,CAA	235.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-5.910e-01;ClippingRankSum=-2.600e-01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.16;MQRankSum=0.827;QD=8.71;ReadPosRankSum=-1.470e-01;SOR=0.495	GT:AD:DP:GQ:PL	1/2:7,13,7:31:41:252,41,376,147,0,361
-20	10077752	.	T	C	1366.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.391e+00;ClippingRankSum=-9.460e-01;DP=79;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-3.420e-01;QD=17.30;ReadPosRankSum=0.698;SOR=1.251	GT:AD:DP:GQ:PL	0/1:34,45:79:99:1374,0,1187
-20	10079476	.	T	G	31.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.310e+00;ClippingRankSum=-5.690e-01;DP=44;ExcessHet=3.0103;FS=57.922;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-3.250e-01;QD=0.72;ReadPosRankSum=-4.174e+00;SOR=4.970	GT:AD:DP:GQ:PL	0/1:33,11:44:39:39,0,1137
-20	10081750	.	C	A	1374.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=0.552;DP=83;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.41;QD=16.56;ReadPosRankSum=0.525;SOR=0.664	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1382,0,1525
-20	10081800	.	C	T	1130.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;ClippingRankSum=-5.030e-01;DP=68;ExcessHet=3.0103;FS=11.086;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.03;QD=16.63;ReadPosRankSum=0.957;SOR=0.143	GT:AD:DP:GQ:PL	0/1:35,33:68:99:1138,0,1222
-20	10082892	.	C	T	1727.03	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=31.88;SOR=0.883	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,44:44:99:1|1:10082885_A_C:1741,132,0
-20	10085211	.	A	T	1231.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.306e+00;ClippingRankSum=0.785;DP=77;ExcessHet=3.0103;FS=0.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-8.060e-01;QD=16.21;ReadPosRankSum=1.29;SOR=0.723	GT:AD:DP:GQ:PL	0/1:40,36:76:99:1239,0,1443
-20	10086110	.	G	A	1295.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.890e-01;ClippingRankSum=-7.620e-01;DP=81;ExcessHet=3.0103;FS=1.810;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=2.07;QD=16.00;ReadPosRankSum=2.30;SOR=0.495	GT:AD:DP:GQ:PL	0/1:43,38:81:99:1303,0,1506
-20	10086283	.	G	T	1046.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.34;ClippingRankSum=0.180;DP=85;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.622;QD=12.46;ReadPosRankSum=2.11;SOR=0.529	GT:AD:DP:GQ:PL	0/1:52,32:84:99:1054,0,1771
-20	10086619	.	T	A	817.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;ClippingRankSum=0.539;DP=71;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-3.800e-01;QD=11.68;ReadPosRankSum=0.282;SOR=0.846	GT:AD:DP:GQ:PL	0/1:45,25:70:99:825,0,1603
-20	10086853	.	G	A	1023.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.87;ClippingRankSum=0.128;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=0.261;QD=14.02;ReadPosRankSum=-2.060e-01;SOR=0.767	GT:AD:DP:GQ:PL	0/1:41,32:73:99:1031,0,1280
-20	10086954	.	G	A	1116.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.58;ClippingRankSum=-1.012e+00;DP=68;ExcessHet=3.0103;FS=4.812;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.521;QD=16.42;ReadPosRankSum=-1.290e-01;SOR=1.185	GT:AD:DP:GQ:PL	0/1:34,34:68:99:1124,0,1051
-20	10087230	.	A	G	1863.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.072e+00;ClippingRankSum=0.462;DP=96;ExcessHet=3.0103;FS=3.860;MLEAC=1;MLEAF=0.500;MQ=58.88;MQRankSum=1.50;QD=19.41;ReadPosRankSum=1.01;SOR=0.960	GT:AD:DP:GQ:PL	0/1:42,54:96:99:1871,0,1428
-20	10087394	.	T	G	1709.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.159e+00;ClippingRankSum=-1.579e+00;DP=84;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.236;QD=20.35;ReadPosRankSum=0.871;SOR=0.436	GT:AD:DP:GQ:PL	0/1:35,49:84:99:1717,0,1186
-20	10087754	.	T	G	1368.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;ClippingRankSum=-1.031e+00;DP=79;ExcessHet=3.0103;FS=0.869;MLEAC=1;MLEAF=0.500;MQ=60.39;MQRankSum=0.420;QD=17.55;ReadPosRankSum=-8.510e-01;SOR=0.562	GT:AD:DP:GQ:PL	0/1:37,41:78:99:1376,0,1239
-20	10087804	.	C	T	1640.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.01;ClippingRankSum=0.817;DP=100;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.77;MQRankSum=1.39;QD=16.41;ReadPosRankSum=1.02;SOR=0.369	GT:AD:DP:GQ:PL	0/1:50,50:100:99:1648,0,1511
-20	10087820	.	C	CAG	458.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.662e+00;ClippingRankSum=-6.860e-01;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.53;MQRankSum=0.592;QD=8.65;ReadPosRankSum=9.000e-03;SOR=0.850	GT:AD:DP:GQ:PL	0/1:35,18:53:99:466,0,1168
-20	10088063	.	C	T	1438.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.37;ClippingRankSum=-3.660e-01;DP=93;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=-1.535e+00;QD=15.47;ReadPosRankSum=0.081;SOR=1.053	GT:AD:DP:GQ:PL	0/1:49,44:93:99:1446,0,1403
-20	10088699	.	C	T	797.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.52;ClippingRankSum=0.050;DP=63;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=-5.000e-02;QD=12.86;ReadPosRankSum=-2.350e-01;SOR=1.914	GT:AD:DP:GQ:PL	0/1:36,26:62:99:805,0,1088
-20	10088730	.	G	A	993.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;ClippingRankSum=-9.210e-01;DP=53;ExcessHet=3.0103;FS=15.383;MLEAC=1;MLEAF=0.500;MQ=53.06;MQRankSum=-2.543e+00;QD=19.11;ReadPosRankSum=0.461;SOR=1.592	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,23:52:99:0|1:10088730_G_A:1001,0,1152
-20	10088736	.	A	C	1102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;ClippingRankSum=2.03;DP=56;ExcessHet=3.0103;FS=9.673;MLEAC=1;MLEAF=0.500;MQ=51.85;MQRankSum=-3.275e+00;QD=20.05;ReadPosRankSum=-5.900e-02;SOR=0.851	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,27:55:99:0|1:10088730_G_A:1110,0,1194
-20	10088747	.	A	G	1132.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.851e+00;ClippingRankSum=0.538;DP=56;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.25;MQRankSum=-3.140e+00;QD=20.97;ReadPosRankSum=-3.820e-01;SOR=1.092	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,29:54:99:0|1:10088730_G_A:1140,0,995
-20	10088799	.	G	A	1039.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.37;ClippingRankSum=0.262;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-1.309e+00;QD=19.62;ReadPosRankSum=0.930;SOR=1.003	GT:AD:DP:GQ:PL	0/1:22,31:53:99:1047,0,617
-20	10088895	.	C	T	553.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.43;ClippingRankSum=1.04;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.76;MQRankSum=1.09;QD=13.50;ReadPosRankSum=0.933;SOR=0.653	GT:AD:DP:GQ:PL	0/1:23,18:41:99:561,0,673
-20	10088968	.	C	CAAA	1205.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;ClippingRankSum=0.296;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-3.024e+00;QD=22.75;ReadPosRankSum=0.960;SOR=1.012	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367
-20	10088980	.	T	C	1268.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.662e+00;ClippingRankSum=0.197;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-4.162e+00;QD=18.66;ReadPosRankSum=1.12;SOR=0.709	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627
-20	10088985	.	T	C	1199.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.560e-01;ClippingRankSum=-8.890e-01;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-4.381e+00;QD=16.21;ReadPosRankSum=1.39;SOR=0.742	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729
-20	10089441	.	A	G	1200.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.770e+00;ClippingRankSum=-1.652e+00;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.177;QD=15.80;ReadPosRankSum=1.29;SOR=1.363	GT:AD:DP:GQ:PL	0/1:37,39:76:99:1208,0,1313
-20	10089525	.	C	T	1569.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.71;ClippingRankSum=0.412;DP=82;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=1.57;QD=19.38;ReadPosRankSum=1.27;SOR=0.617	GT:AD:DP:GQ:PL	0/1:38,43:81:99:1577,0,1088
-20	10090289	.	CA	C	414.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;ClippingRankSum=1.20;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=-2.870e-01;QD=12.20;ReadPosRankSum=-2.700e-01;SOR=0.859	GT:AD:DP:GQ:PL	0/1:14,20:38:99:422,0,230
-20	10090764	.	A	G	861.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.696e+00;ClippingRankSum=1.19;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.000e-03;QD=13.68;ReadPosRankSum=1.54;SOR=0.310	GT:AD:DP:GQ:PL	0/1:34,29:63:99:869,0,1207
-20	10090970	.	T	C	1278.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.950e-01;ClippingRankSum=-1.260e-01;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.90;QD=18.53;ReadPosRankSum=1.53;SOR=0.518	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1286,0,1092
-20	10091214	.	C	T	1270.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.518;ClippingRankSum=-9.180e-01;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.635;QD=18.15;ReadPosRankSum=1.73;SOR=0.625	GT:AD:DP:GQ:PL	0/1:33,37:70:99:1278,0,1110
-20	10092415	.	A	G	1656.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.669e+00;ClippingRankSum=-1.063e+00;DP=102;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.438;QD=16.40;ReadPosRankSum=0.622;SOR=0.665	GT:AD:DP:GQ:PL	0/1:52,49:101:99:1664,0,1902
-20	10092927	.	G	T	127.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.416e+00;ClippingRankSum=-7.610e-01;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=0.322;QD=1.77;ReadPosRankSum=-3.997e+00;SOR=5.279	GT:AD:DP:GQ:PL	0/1:59,13:72:99:135,0,1864
-20	10093568	.	GT	G	356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.487;ClippingRankSum=0.692;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=-1.384e+00;QD=10.49;ReadPosRankSum=1.02;SOR=0.751	GT:AD:DP:GQ:PL	0/1:17,17:42:99:364,0,386
-20	10093923	.	T	A	1096.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080e-01;ClippingRankSum=-1.690e-01;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=1.29;QD=16.37;ReadPosRankSum=-2.450e-01;SOR=0.772	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1104,0,1257
-20	10094251	.	T	A	1291.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;ClippingRankSum=-1.120e+00;DP=63;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.235;QD=20.83;ReadPosRankSum=2.29;SOR=1.211	GT:AD:DP:GQ:PL	0/1:26,36:62:99:1299,0,781
-20	10094582	.	A	G	944.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.325e+00;ClippingRankSum=-2.840e-01;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=1.28;QD=13.69;ReadPosRankSum=0.272;SOR=0.772	GT:AD:DP:GQ:PL	0/1:39,30:69:99:952,0,1350
-20	10094774	.	C	T	1057.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.850e-01;ClippingRankSum=-1.620e+00;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-3.240e-01;QD=14.10;ReadPosRankSum=0.982;SOR=0.690	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1065,0,1282
+20	10076250	.	A	G	1128.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.319e+00;ClippingRankSum=0.260;DP=80;ExcessHet=3.0103;FS=7.546;MLEAC=1;MLEAF=0.500;MQ=59.40;MQRankSum=0.387;QD=14.29;ReadPosRankSum=-5.000e-03;SOR=0.344	GT:AD:DP:GQ:PL	0/1:40,39:79:99:1136,0,1339
+20	10076339	.	A	G	1330.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.028;ClippingRankSum=1.23;DP=72;ExcessHet=3.0103;FS=1.992;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=-1.700e-02;QD=18.48;ReadPosRankSum=0.833;SOR=0.446	GT:AD:DP:GQ:PL	0/1:32,40:72:99:1338,0,1035
+20	10076399	.	G	A	1828.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.85;ClippingRankSum=0.974;DP=94;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.959;QD=19.45;ReadPosRankSum=-7.990e-01;SOR=0.952	GT:AD:DP:GQ:PL	0/1:44,50:94:99:1836,0,1544
+20	10076989	.	CA	C,CAA	235.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-5.910e-01;ClippingRankSum=-2.600e-01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.16;MQRankSum=0.827;QD=8.70;ReadPosRankSum=-1.470e-01;SOR=0.495	GT:AD:DP:GQ:PL	1/2:7,13,7:31:41:252,41,376,147,0,361
+20	10077752	.	T	C	1366.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.391e+00;ClippingRankSum=-9.460e-01;DP=79;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-3.420e-01;QD=17.30;ReadPosRankSum=0.698;SOR=1.251	GT:AD:DP:GQ:PL	0/1:34,45:79:99:1374,0,1187
+20	10079476	.	T	G	31.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.310e+00;ClippingRankSum=-5.690e-01;DP=44;ExcessHet=3.0103;FS=57.922;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-3.250e-01;QD=0.72;ReadPosRankSum=-4.174e+00;SOR=4.970	GT:AD:DP:GQ:PL	0/1:33,11:44:39:39,0,1137
+20	10081750	.	C	A	1374.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=0.552;DP=83;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.41;QD=16.56;ReadPosRankSum=0.525;SOR=0.664	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1382,0,1525
+20	10081800	.	C	T	1130.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;ClippingRankSum=-5.030e-01;DP=68;ExcessHet=3.0103;FS=11.086;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.03;QD=16.63;ReadPosRankSum=0.957;SOR=0.143	GT:AD:DP:GQ:PL	0/1:35,33:68:99:1138,0,1222
+20	10082892	.	C	T	1727.06	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=31.88;SOR=0.883	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,44:44:99:1|1:10082885_A_C:1741,132,0
+20	10085211	.	A	T	1231.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.306e+00;ClippingRankSum=0.785;DP=77;ExcessHet=3.0103;FS=0.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-8.060e-01;QD=16.21;ReadPosRankSum=1.29;SOR=0.723	GT:AD:DP:GQ:PL	0/1:40,36:76:99:1239,0,1443
+20	10086110	.	G	A	1295.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.890e-01;ClippingRankSum=-7.620e-01;DP=81;ExcessHet=3.0103;FS=1.810;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=2.07;QD=16.00;ReadPosRankSum=2.30;SOR=0.495	GT:AD:DP:GQ:PL	0/1:43,38:81:99:1303,0,1506
+20	10086283	.	G	T	1046.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.34;ClippingRankSum=0.180;DP=85;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.622;QD=12.46;ReadPosRankSum=2.11;SOR=0.529	GT:AD:DP:GQ:PL	0/1:52,32:84:99:1054,0,1771
+20	10086619	.	T	A	817.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;ClippingRankSum=0.539;DP=71;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-3.800e-01;QD=11.68;ReadPosRankSum=0.282;SOR=0.846	GT:AD:DP:GQ:PL	0/1:45,25:70:99:825,0,1603
+20	10086853	.	G	A	1023.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.87;ClippingRankSum=0.128;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=0.261;QD=14.02;ReadPosRankSum=-2.060e-01;SOR=0.767	GT:AD:DP:GQ:PL	0/1:41,32:73:99:1031,0,1280
+20	10086954	.	G	A	1116.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.58;ClippingRankSum=-1.012e+00;DP=68;ExcessHet=3.0103;FS=4.812;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.521;QD=16.42;ReadPosRankSum=-1.290e-01;SOR=1.185	GT:AD:DP:GQ:PL	0/1:34,34:68:99:1124,0,1051
+20	10087230	.	A	G	1863.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.072e+00;ClippingRankSum=0.462;DP=96;ExcessHet=3.0103;FS=3.860;MLEAC=1;MLEAF=0.500;MQ=58.88;MQRankSum=1.50;QD=19.41;ReadPosRankSum=1.01;SOR=0.960	GT:AD:DP:GQ:PL	0/1:42,54:96:99:1871,0,1428
+20	10087394	.	T	G	1709.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.159e+00;ClippingRankSum=-1.579e+00;DP=84;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.236;QD=20.35;ReadPosRankSum=0.871;SOR=0.436	GT:AD:DP:GQ:PL	0/1:35,49:84:99:1717,0,1186
+20	10087754	.	T	G	1368.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;ClippingRankSum=-1.031e+00;DP=79;ExcessHet=3.0103;FS=0.869;MLEAC=1;MLEAF=0.500;MQ=60.39;MQRankSum=0.420;QD=17.55;ReadPosRankSum=-8.510e-01;SOR=0.562	GT:AD:DP:GQ:PL	0/1:37,41:78:99:1376,0,1239
+20	10087804	.	C	T	1640.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.01;ClippingRankSum=0.817;DP=100;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.77;MQRankSum=1.39;QD=16.41;ReadPosRankSum=1.02;SOR=0.369	GT:AD:DP:GQ:PL	0/1:50,50:100:99:1648,0,1511
+20	10087820	.	C	CAG	458.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.662e+00;ClippingRankSum=-6.860e-01;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.53;MQRankSum=0.592;QD=8.65;ReadPosRankSum=9.000e-03;SOR=0.850	GT:AD:DP:GQ:PL	0/1:35,18:53:99:466,0,1168
+20	10088063	.	C	T	1438.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.37;ClippingRankSum=-3.660e-01;DP=93;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=-1.535e+00;QD=15.47;ReadPosRankSum=0.081;SOR=1.053	GT:AD:DP:GQ:PL	0/1:49,44:93:99:1446,0,1403
+20	10088699	.	C	T	797.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.52;ClippingRankSum=0.050;DP=63;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=-5.000e-02;QD=12.87;ReadPosRankSum=-2.350e-01;SOR=1.914	GT:AD:DP:GQ:PL	0/1:36,26:62:99:805,0,1088
+20	10088730	.	G	A	993.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;ClippingRankSum=-9.210e-01;DP=53;ExcessHet=3.0103;FS=15.383;MLEAC=1;MLEAF=0.500;MQ=53.06;MQRankSum=-2.543e+00;QD=19.11;ReadPosRankSum=0.461;SOR=1.592	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,23:52:99:0|1:10088730_G_A:1001,0,1152
+20	10088736	.	A	C	1102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;ClippingRankSum=2.03;DP=56;ExcessHet=3.0103;FS=9.673;MLEAC=1;MLEAF=0.500;MQ=51.85;MQRankSum=-3.275e+00;QD=20.05;ReadPosRankSum=-5.900e-02;SOR=0.851	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,27:55:99:0|1:10088730_G_A:1110,0,1194
+20	10088747	.	A	G	1132.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.851e+00;ClippingRankSum=0.538;DP=56;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.25;MQRankSum=-3.140e+00;QD=20.97;ReadPosRankSum=-3.820e-01;SOR=1.092	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,29:54:99:0|1:10088730_G_A:1140,0,995
+20	10088799	.	G	A	1039.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.37;ClippingRankSum=0.262;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-1.309e+00;QD=19.62;ReadPosRankSum=0.930;SOR=1.003	GT:AD:DP:GQ:PL	0/1:22,31:53:99:1047,0,617
+20	10088895	.	C	T	553.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.43;ClippingRankSum=1.04;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.76;MQRankSum=1.09;QD=13.50;ReadPosRankSum=0.933;SOR=0.653	GT:AD:DP:GQ:PL	0/1:23,18:41:99:561,0,673
+20	10088968	.	C	CAAA	1205.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;ClippingRankSum=0.296;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-3.024e+00;QD=22.75;ReadPosRankSum=0.960;SOR=1.012	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367
+20	10088980	.	T	C	1268.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.662e+00;ClippingRankSum=0.197;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-4.162e+00;QD=18.66;ReadPosRankSum=1.12;SOR=0.709	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627
+20	10088985	.	T	C	1199.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.560e-01;ClippingRankSum=-8.890e-01;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-4.381e+00;QD=16.21;ReadPosRankSum=1.39;SOR=0.742	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729
+20	10089441	.	A	G	1200.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.770e+00;ClippingRankSum=-1.652e+00;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.177;QD=15.80;ReadPosRankSum=1.29;SOR=1.363	GT:AD:DP:GQ:PL	0/1:37,39:76:99:1208,0,1313
+20	10089525	.	C	T	1569.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.71;ClippingRankSum=0.412;DP=82;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=1.57;QD=19.38;ReadPosRankSum=1.27;SOR=0.617	GT:AD:DP:GQ:PL	0/1:38,43:81:99:1577,0,1088
+20	10090289	.	CA	C	414.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;ClippingRankSum=1.20;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=-2.870e-01;QD=12.19;ReadPosRankSum=-2.700e-01;SOR=0.859	GT:AD:DP:GQ:PL	0/1:14,20:38:99:422,0,230
+20	10090764	.	A	G	861.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.696e+00;ClippingRankSum=1.19;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.000e-03;QD=13.68;ReadPosRankSum=1.54;SOR=0.310	GT:AD:DP:GQ:PL	0/1:34,29:63:99:869,0,1207
+20	10090970	.	T	C	1278.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.950e-01;ClippingRankSum=-1.260e-01;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.90;QD=18.53;ReadPosRankSum=1.53;SOR=0.518	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1286,0,1092
+20	10091214	.	C	T	1270.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.518;ClippingRankSum=-9.180e-01;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.635;QD=18.15;ReadPosRankSum=1.73;SOR=0.625	GT:AD:DP:GQ:PL	0/1:33,37:70:99:1278,0,1110
+20	10092415	.	A	G	1656.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.669e+00;ClippingRankSum=-1.063e+00;DP=102;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.438;QD=16.40;ReadPosRankSum=0.622;SOR=0.665	GT:AD:DP:GQ:PL	0/1:52,49:101:99:1664,0,1902
+20	10092927	.	G	T	127.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.416e+00;ClippingRankSum=-7.610e-01;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=0.322;QD=1.77;ReadPosRankSum=-3.997e+00;SOR=5.279	GT:AD:DP:GQ:PL	0/1:59,13:72:99:135,0,1864
+20	10093568	.	GT	G	356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.487;ClippingRankSum=0.692;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=-1.384e+00;QD=10.49;ReadPosRankSum=1.02;SOR=0.751	GT:AD:DP:GQ:PL	0/1:17,17:42:99:364,0,386
+20	10093923	.	T	A	1096.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080e-01;ClippingRankSum=-1.690e-01;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=1.29;QD=16.37;ReadPosRankSum=-2.450e-01;SOR=0.772	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1104,0,1257
+20	10094251	.	T	A	1291.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;ClippingRankSum=-1.120e+00;DP=63;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.235;QD=20.83;ReadPosRankSum=2.29;SOR=1.211	GT:AD:DP:GQ:PL	0/1:26,36:62:99:1299,0,781
+20	10094582	.	A	G	944.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.325e+00;ClippingRankSum=-2.840e-01;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=1.28;QD=13.69;ReadPosRankSum=0.272;SOR=0.772	GT:AD:DP:GQ:PL	0/1:39,30:69:99:952,0,1350
+20	10094774	.	C	T	1057.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.850e-01;ClippingRankSum=-1.620e+00;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-3.240e-01;QD=14.10;ReadPosRankSum=0.982;SOR=0.690	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1065,0,1282
 20	10095432	.	GTGATGATGA	G	869.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.32;ClippingRankSum=-5.060e-01;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-3.951e+00;QD=17.39;ReadPosRankSum=0.659;SOR=0.460	GT:AD:DP:GQ:PL	0/1:27,23:50:99:877,0,2108
-20	10095741	.	A	G	1096.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.580e-01;ClippingRankSum=-4.880e-01;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-4.990e-01;QD=15.67;ReadPosRankSum=1.19;SOR=0.515	GT:AD:DP:GQ:PL	0/1:36,34:70:99:1104,0,1233
-20	10096293	.	C	T	1376.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.49;ClippingRankSum=0.048;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQRankSum=0.609;QD=18.35;ReadPosRankSum=-1.220e-01;SOR=0.638	GT:AD:DP:GQ:PL	0/1:37,38:75:99:1384,0,1258
-20	10096596	.	C	T	1583.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.41;ClippingRankSum=-2.430e-01;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.141;QD=18.20;ReadPosRankSum=1.07;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,47:87:99:1591,0,1273
-20	10096768	.	A	C	1703.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.201e+00;ClippingRankSum=-7.130e-01;DP=91;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=-2.350e-01;QD=18.72;ReadPosRankSum=0.967;SOR=0.445	GT:AD:DP:GQ:PL	0/1:42,49:91:99:1711,0,1452
-20	10096899	.	G	T	1635.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.86;ClippingRankSum=-9.660e-01;DP=79;ExcessHet=3.0103;FS=9.606;MLEAC=1;MLEAF=0.500;MQ=59.53;MQRankSum=0.328;QD=20.70;ReadPosRankSum=0.407;SOR=1.707	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,40:79:99:0|1:10096899_G_T:1643,0,1520
+20	10095741	.	A	G	1096.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.580e-01;ClippingRankSum=-4.880e-01;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-4.990e-01;QD=15.67;ReadPosRankSum=1.19;SOR=0.515	GT:AD:DP:GQ:PL	0/1:36,34:70:99:1104,0,1233
+20	10096293	.	C	T	1376.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.49;ClippingRankSum=0.048;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQRankSum=0.609;QD=18.36;ReadPosRankSum=-1.220e-01;SOR=0.638	GT:AD:DP:GQ:PL	0/1:37,38:75:99:1384,0,1258
+20	10096596	.	C	T	1583.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.41;ClippingRankSum=-2.430e-01;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.141;QD=18.20;ReadPosRankSum=1.07;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,47:87:99:1591,0,1273
+20	10096768	.	A	C	1703.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.201e+00;ClippingRankSum=-7.130e-01;DP=91;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=-2.350e-01;QD=18.72;ReadPosRankSum=0.967;SOR=0.445	GT:AD:DP:GQ:PL	0/1:42,49:91:99:1711,0,1452
+20	10096899	.	G	T	1635.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.86;ClippingRankSum=-9.660e-01;DP=79;ExcessHet=3.0103;FS=9.606;MLEAC=1;MLEAF=0.500;MQ=59.53;MQRankSum=0.328;QD=20.70;ReadPosRankSum=0.407;SOR=1.707	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,40:79:99:0|1:10096899_G_T:1643,0,1520
 20	10096905	.	TA	T	1630.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.162e+00;ClippingRankSum=-9.600e-02;DP=83;ExcessHet=3.0103;FS=11.159;MLEAC=1;MLEAF=0.500;MQ=59.27;MQRankSum=-3.870e-01;QD=19.65;ReadPosRankSum=0.415;SOR=1.775	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,43:83:99:0|1:10096899_G_T:1638,0,1623
-20	10096933	.	G	C	1532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.851e+00;ClippingRankSum=0.690;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-3.300e-01;QD=18.03;ReadPosRankSum=0.242;SOR=1.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770
-20	10096958	.	G	A	1787.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.41;ClippingRankSum=1.00;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=1.52;QD=19.43;ReadPosRankSum=-1.574e+00;SOR=1.387	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629
-20	10097075	.	T	G	1466.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.278e+00;ClippingRankSum=0.668;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.505e+00;QD=15.94;ReadPosRankSum=-2.850e-01;SOR=0.628	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482
-20	10097101	.	C	CTTT	1121.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.950e-01;ClippingRankSum=0.397;DP=76;ExcessHet=3.0103;FS=5.060;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-8.950e-01;QD=18.69;ReadPosRankSum=1.15;SOR=0.277	GT:AD:DP:GQ:PL	0/1:34,26:64:99:1129,0,1306
+20	10096933	.	G	C	1532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.851e+00;ClippingRankSum=0.690;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-3.300e-01;QD=18.03;ReadPosRankSum=0.242;SOR=1.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770
+20	10096958	.	G	A	1787.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.41;ClippingRankSum=1.00;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=1.52;QD=19.43;ReadPosRankSum=-1.574e+00;SOR=1.387	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629
+20	10097075	.	T	G	1466.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.278e+00;ClippingRankSum=0.668;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.505e+00;QD=15.94;ReadPosRankSum=-2.850e-01;SOR=0.628	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482
+20	10097101	.	C	CTTT	1121.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.950e-01;ClippingRankSum=0.397;DP=76;ExcessHet=3.0103;FS=5.060;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-8.950e-01;QD=18.69;ReadPosRankSum=1.15;SOR=0.277	GT:AD:DP:GQ:PL	0/1:34,26:64:99:1129,0,1306
 20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C	1084.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.91;ClippingRankSum=-5.770e-01;DP=89;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.27;MQRankSum=-4.536e+00;QD=12.19;ReadPosRankSum=-3.198e+00;SOR=0.948	GT:AD:DP:GQ:PGT:PID:PL	0/1:57,32:89:99:0|1:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:1092,0,2241
 20	10097437	.	TTTTC	T	826.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.589;ClippingRankSum=-4.010e-01;DP=76;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=53.48;MQRankSum=4.19;QD=15.03;ReadPosRankSum=2.91;SOR=1.382	GT:AD:DP:GQ:PGT:PID:PL	0/1:32,23:55:99:1|0:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:834,0,1193
-20	10097626	.	C	A	647.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.993;ClippingRankSum=-3.030e-01;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-5.960e-01;QD=13.49;ReadPosRankSum=1.89;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957
-20	10097789	.	T	C	709.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.017e+00;ClippingRankSum=-7.890e-01;DP=61;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=57.89;MQRankSum=0.333;QD=12.45;ReadPosRankSum=1.44;SOR=0.756	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190
-20	10097928	.	G	A	591.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.870e-01;ClippingRankSum=1.58;DP=40;ExcessHet=3.0103;FS=1.315;MLEAC=1;MLEAF=0.500;MQ=58.25;MQRankSum=0.095;QD=16.43;ReadPosRankSum=-2.540e-01;SOR=0.951	GT:AD:DP:GQ:PL	0/1:17,19:36:99:599,0,586
-20	10098110	.	G	C	607.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.47;ClippingRankSum=0.158;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=0.761;QD=16.88;ReadPosRankSum=-7.610e-01;SOR=0.069	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,17:36:99:0|1:10098110_G_C:615,0,727
-20	10098135	.	C	A	492.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.316e+00;ClippingRankSum=-8.020e-01;DP=38;ExcessHet=3.0103;FS=4.337;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=0.409;QD=12.96;ReadPosRankSum=-6.510e-01;SOR=0.075	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,14:38:99:0|1:10098110_G_C:500,0,964
+20	10097626	.	C	A	647.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.993;ClippingRankSum=-3.030e-01;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-5.960e-01;QD=13.49;ReadPosRankSum=1.89;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957
+20	10097789	.	T	C	709.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.017e+00;ClippingRankSum=-7.890e-01;DP=61;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=57.89;MQRankSum=0.333;QD=12.45;ReadPosRankSum=1.44;SOR=0.756	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190
+20	10097928	.	G	A	591.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.870e-01;ClippingRankSum=1.58;DP=40;ExcessHet=3.0103;FS=1.315;MLEAC=1;MLEAF=0.500;MQ=58.25;MQRankSum=0.095;QD=16.43;ReadPosRankSum=-2.540e-01;SOR=0.951	GT:AD:DP:GQ:PL	0/1:17,19:36:99:599,0,586
+20	10098110	.	G	C	607.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.47;ClippingRankSum=0.158;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=0.761;QD=16.88;ReadPosRankSum=-7.610e-01;SOR=0.069	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,17:36:99:0|1:10098110_G_C:615,0,727
+20	10098135	.	C	A	492.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.316e+00;ClippingRankSum=-8.020e-01;DP=38;ExcessHet=3.0103;FS=4.337;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=0.409;QD=12.96;ReadPosRankSum=-6.510e-01;SOR=0.075	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,14:38:99:0|1:10098110_G_C:500,0,964
 20	10098219	.	TATATATA	T	325.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.66;ClippingRankSum=-1.173e+00;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.94;MQRankSum=-6.040e-01;QD=15.50;ReadPosRankSum=0.462;SOR=0.465	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,9:21:99:0|1:10098219_TATATATA_T:333,0,461
-20	10098237	.	A	T	265.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;ClippingRankSum=-9.350e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.40;MQRankSum=-1.493e+00;QD=20.43;ReadPosRankSum=1.41;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273
-20	10098265	.	T	C	154.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=-1.380e+00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.380e+00;QD=25.77;ReadPosRankSum=0.358;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59
-20	10098885	.	C	CA	463.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.615;ClippingRankSum=-2.124e+00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.89;MQRankSum=-4.069e+00;QD=14.96;ReadPosRankSum=-1.790e-01;SOR=0.518	GT:AD:DP:GQ:PL	0/1:17,14:31:99:471,0,572
-20	10098945	.	T	C	473.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=-5.340e-01;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.137e+00;QD=21.53;ReadPosRankSum=0.801;SOR=2.368	GT:AD:DP:GQ:PL	0/1:9,13:22:99:481,0,248
-20	10098987	.	C	T	400.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.90;ClippingRankSum=0.695;DP=24;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.88;MQRankSum=-1.912e+00;QD=16.69;ReadPosRankSum=0.290;SOR=2.925	GT:AD:DP:GQ:PL	0/1:11,13:24:99:408,0,350
-20	10099029	.	T	C	355.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.702e+00;ClippingRankSum=1.17;DP=28;ExcessHet=3.0103;FS=2.032;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-2.901e+00;QD=12.70;ReadPosRankSum=-8.870e-01;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
-20	10099034	.	C	A	355.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=-3.120e-01;DP=28;ExcessHet=3.0103;FS=4.265;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-2.469e+00;QD=12.70;ReadPosRankSum=-1.558e+00;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
-20	10099044	.	A	C	355.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073e+00;ClippingRankSum=-7.750e-01;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-3.995e+00;QD=14.82;ReadPosRankSum=-2.683e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:363,0,768
-20	10099046	.	T	C	325.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.027e+00;ClippingRankSum=-3.580e-01;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-3.995e+00;QD=13.57;ReadPosRankSum=-2.743e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:333,0,603
-20	10099055	.	T	C	277.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.581e+00;ClippingRankSum=0.613;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.46;MQRankSum=-3.841e+00;QD=12.07;ReadPosRankSum=-2.162e+00;SOR=0.665	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,8:23:99:0|1:10099029_T_C:285,0,673
-20	10099079	.	C	T	137.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=0.619;DP=29;ExcessHet=3.0103;FS=1.862;MLEAC=1;MLEAF=0.500;MQ=52.09;MQRankSum=-2.342e+00;QD=4.74;ReadPosRankSum=1.91;SOR=1.289	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,6:29:99:0|1:10099029_T_C:145,0,886
-20	10099111	.	T	TTTTGTTTG	686.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314e+00;ClippingRankSum=0.188;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.12;MQRankSum=-3.909e+00;QD=19.62;ReadPosRankSum=-8.500e-02;SOR=0.511	GT:AD:DP:GQ:PL	0/1:22,13:35:99:694,0,802
-20	10099140	.	G	T	1026.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.610e-01;ClippingRankSum=0.204;DP=62;ExcessHet=3.0103;FS=2.241;MLEAC=1;MLEAF=0.500;MQ=55.72;MQRankSum=-1.754e+00;QD=16.56;ReadPosRankSum=0.176;SOR=1.114	GT:AD:DP:GQ:PL	0/1:30,32:62:99:1034,0,931
-20	10099190	.	G	T	1055.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.260e-01;ClippingRankSum=0.295;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQRankSum=-1.161e+00;QD=16.24;ReadPosRankSum=-4.530e-01;SOR=0.776	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1063,0,1154
-20	10099220	.	A	G	598.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.610e+00;ClippingRankSum=0.103;DP=45;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-1.610e+00;QD=13.30;ReadPosRankSum=0.286;SOR=0.519	GT:AD:DP:GQ:PL	0/1:25,20:45:99:606,0,873
-20	10099250	.	G	A	720.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.05;ClippingRankSum=-2.300e-01;DP=37;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.71;MQRankSum=-1.119e+00;QD=19.48;ReadPosRankSum=0.199;SOR=0.162	GT:AD:DP:GQ:PL	0/1:16,21:37:99:728,0,424
-20	10099535	.	G	A	1356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.99;ClippingRankSum=-2.340e-01;DP=65;ExcessHet=3.0103;FS=2.172;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-3.280e-01;QD=20.87;ReadPosRankSum=-4.700e-02;SOR=0.408	GT:AD:DP:GQ:PL	0/1:26,39:65:99:1364,0,686
-20	10099565	.	C	T	1367.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.58;ClippingRankSum=-1.800e-02;DP=69;ExcessHet=3.0103;FS=8.736;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-8.500e-01;QD=19.82;ReadPosRankSum=1.68;SOR=0.191	GT:AD:DP:GQ:PL	0/1:31,38:69:99:1375,0,994
-20	10099755	.	C	T	1119.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.58;ClippingRankSum=-6.890e-01;DP=66;ExcessHet=3.0103;FS=2.074;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-7.280e-01;QD=17.22;ReadPosRankSum=0.361;SOR=0.446	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1127,0,1148
-20	10099832	.	A	G	1094.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.724e+00;ClippingRankSum=-4.520e-01;DP=72;ExcessHet=3.0103;FS=4.632;MLEAC=1;MLEAF=0.500;MQ=58.96;MQRankSum=0.836;QD=15.20;ReadPosRankSum=1.67;SOR=0.871	GT:AD:DP:GQ:PL	0/1:39,33:72:99:1102,0,1430
-20	10100468	.	T	C	897.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.064e+00;ClippingRankSum=0.467;DP=64;ExcessHet=3.0103;FS=3.431;MLEAC=1;MLEAF=0.500;MQ=58.38;MQRankSum=-1.960e-01;QD=14.03;ReadPosRankSum=-8.320e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:36,28:64:99:905,0,1299
+20	10098237	.	A	T	265.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;ClippingRankSum=-9.350e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.40;MQRankSum=-1.493e+00;QD=20.43;ReadPosRankSum=1.41;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273
+20	10098265	.	T	C	154.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=-1.380e+00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.380e+00;QD=25.77;ReadPosRankSum=0.358;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59
+20	10098885	.	C	CA	463.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.615;ClippingRankSum=-2.124e+00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.89;MQRankSum=-4.069e+00;QD=14.95;ReadPosRankSum=-1.790e-01;SOR=0.518	GT:AD:DP:GQ:PL	0/1:17,14:31:99:471,0,572
+20	10098945	.	T	C	473.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=-5.340e-01;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.137e+00;QD=21.53;ReadPosRankSum=0.801;SOR=2.368	GT:AD:DP:GQ:PL	0/1:9,13:22:99:481,0,248
+20	10098987	.	C	T	400.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.90;ClippingRankSum=0.695;DP=24;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.88;MQRankSum=-1.912e+00;QD=16.69;ReadPosRankSum=0.290;SOR=2.925	GT:AD:DP:GQ:PL	0/1:11,13:24:99:408,0,350
+20	10099029	.	T	C	355.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.702e+00;ClippingRankSum=1.17;DP=28;ExcessHet=3.0103;FS=2.032;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-2.901e+00;QD=12.70;ReadPosRankSum=-8.870e-01;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
+20	10099034	.	C	A	355.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=-3.120e-01;DP=28;ExcessHet=3.0103;FS=4.265;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-2.469e+00;QD=12.70;ReadPosRankSum=-1.558e+00;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
+20	10099044	.	A	C	355.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073e+00;ClippingRankSum=-7.750e-01;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-3.995e+00;QD=14.82;ReadPosRankSum=-2.683e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:363,0,768
+20	10099046	.	T	C	325.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.027e+00;ClippingRankSum=-3.580e-01;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-3.995e+00;QD=13.57;ReadPosRankSum=-2.743e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:333,0,603
+20	10099055	.	T	C	277.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.581e+00;ClippingRankSum=0.613;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.46;MQRankSum=-3.841e+00;QD=12.07;ReadPosRankSum=-2.162e+00;SOR=0.665	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,8:23:99:0|1:10099029_T_C:285,0,673
+20	10099079	.	C	T	137.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=0.619;DP=29;ExcessHet=3.0103;FS=1.862;MLEAC=1;MLEAF=0.500;MQ=52.09;MQRankSum=-2.342e+00;QD=4.75;ReadPosRankSum=1.91;SOR=1.289	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,6:29:99:0|1:10099029_T_C:145,0,886
+20	10099111	.	T	TTTTGTTTG	686.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314e+00;ClippingRankSum=0.188;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.12;MQRankSum=-3.909e+00;QD=19.62;ReadPosRankSum=-8.500e-02;SOR=0.511	GT:AD:DP:GQ:PL	0/1:22,13:35:99:694,0,802
+20	10099140	.	G	T	1026.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.610e-01;ClippingRankSum=0.204;DP=62;ExcessHet=3.0103;FS=2.241;MLEAC=1;MLEAF=0.500;MQ=55.72;MQRankSum=-1.754e+00;QD=16.56;ReadPosRankSum=0.176;SOR=1.114	GT:AD:DP:GQ:PL	0/1:30,32:62:99:1034,0,931
+20	10099190	.	G	T	1055.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.260e-01;ClippingRankSum=0.295;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQRankSum=-1.161e+00;QD=16.24;ReadPosRankSum=-4.530e-01;SOR=0.776	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1063,0,1154
+20	10099220	.	A	G	598.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.610e+00;ClippingRankSum=0.103;DP=45;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-1.610e+00;QD=13.30;ReadPosRankSum=0.286;SOR=0.519	GT:AD:DP:GQ:PL	0/1:25,20:45:99:606,0,873
+20	10099250	.	G	A	720.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.05;ClippingRankSum=-2.300e-01;DP=37;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.71;MQRankSum=-1.119e+00;QD=19.48;ReadPosRankSum=0.199;SOR=0.162	GT:AD:DP:GQ:PL	0/1:16,21:37:99:728,0,424
+20	10099535	.	G	A	1356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.99;ClippingRankSum=-2.340e-01;DP=65;ExcessHet=3.0103;FS=2.172;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-3.280e-01;QD=20.87;ReadPosRankSum=-4.700e-02;SOR=0.408	GT:AD:DP:GQ:PL	0/1:26,39:65:99:1364,0,686
+20	10099565	.	C	T	1367.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.58;ClippingRankSum=-1.800e-02;DP=69;ExcessHet=3.0103;FS=8.736;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-8.500e-01;QD=19.82;ReadPosRankSum=1.68;SOR=0.191	GT:AD:DP:GQ:PL	0/1:31,38:69:99:1375,0,994
+20	10099755	.	C	T	1119.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.58;ClippingRankSum=-6.890e-01;DP=66;ExcessHet=3.0103;FS=2.074;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-7.280e-01;QD=17.23;ReadPosRankSum=0.361;SOR=0.446	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1127,0,1148
+20	10099832	.	A	G	1094.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.724e+00;ClippingRankSum=-4.520e-01;DP=72;ExcessHet=3.0103;FS=4.632;MLEAC=1;MLEAF=0.500;MQ=58.96;MQRankSum=0.836;QD=15.20;ReadPosRankSum=1.67;SOR=0.871	GT:AD:DP:GQ:PL	0/1:39,33:72:99:1102,0,1430
+20	10100468	.	T	C	897.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.064e+00;ClippingRankSum=0.467;DP=64;ExcessHet=3.0103;FS=3.431;MLEAC=1;MLEAF=0.500;MQ=58.38;MQRankSum=-1.960e-01;QD=14.03;ReadPosRankSum=-8.320e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:36,28:64:99:905,0,1299
 20	10100539	.	CTTCTAG	C	1374.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.481;ClippingRankSum=0.178;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.87;MQRankSum=-4.526e+00;QD=18.58;ReadPosRankSum=-1.780e-01;SOR=0.709	GT:AD:DP:GQ:PL	0/1:38,36:74:99:1382,0,1739
-20	10100845	.	G	C	1144.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.864;DP=76;ExcessHet=3.0103;FS=1.900;MLEAC=1;MLEAF=0.500;MQ=55.34;MQRankSum=-8.850e-01;QD=15.26;ReadPosRankSum=1.21;SOR=0.889	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1152,0,1353
+20	10100845	.	G	C	1144.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.864;DP=76;ExcessHet=3.0103;FS=1.900;MLEAC=1;MLEAF=0.500;MQ=55.34;MQRankSum=-8.850e-01;QD=15.26;ReadPosRankSum=1.21;SOR=0.889	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1152,0,1353
 20	10101268	.	TAA	T	890.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;ClippingRankSum=-1.539e+00;DP=70;ExcessHet=3.0103;FS=0.990;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-5.760e-01;QD=14.60;ReadPosRankSum=1.57;SOR=0.870	GT:AD:DP:GQ:PL	0/1:35,26:61:99:898,0,1254
-20	10101288	.	A	G	1006.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.190e-01;ClippingRankSum=1.08;DP=68;ExcessHet=3.0103;FS=2.070;MLEAC=1;MLEAF=0.500;MQ=58.42;MQRankSum=0.517;QD=14.80;ReadPosRankSum=-1.128e+00;SOR=1.040	GT:AD:DP:GQ:PL	0/1:37,31:68:99:1014,0,1275
-20	10101674	.	TTGTG	T,TTGTGTGTGTG	1464.10	.	AC=1,1;AF=0.500,0.500;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.50;QD=30.31;SOR=1.002	GT:AD:DP:GQ:PL	1/2:0,22,6:35:99:1481,557,581,932,0,925
-20	10101880	.	A	G	1599.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.769e+00;ClippingRankSum=-6.570e-01;DP=84;ExcessHet=3.0103;FS=1.801;MLEAC=1;MLEAF=0.500;MQ=59.22;MQRankSum=0.207;QD=19.27;ReadPosRankSum=-1.953e+00;SOR=0.736	GT:AD:DP:GQ:PL	0/1:36,47:83:99:1607,0,1223
-20	10101912	.	C	T	1588.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=0.093;DP=86;ExcessHet=3.0103;FS=0.811;MLEAC=1;MLEAF=0.500;MQ=58.69;MQRankSum=0.569;QD=18.69;ReadPosRankSum=-4.720e-01;SOR=0.604	GT:AD:DP:GQ:PL	0/1:39,46:85:99:1596,0,1309
-20	10102234	.	C	T	1259.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.298e+00;ClippingRankSum=-5.690e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQRankSum=0.093;QD=22.90;ReadPosRankSum=0.840;SOR=0.711	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,31:55:99:0|1:10102234_C_T:1267,0,2599
-20	10102247	.	G	A	1299.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.40;ClippingRankSum=0.144;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQRankSum=0.433;QD=23.63;ReadPosRankSum=1.47;SOR=0.711	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,31:55:99:0|1:10102234_C_T:1307,0,2634
-20	10102248	.	T	C	1299.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.970e-01;ClippingRankSum=0.396;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.95;MQRankSum=-9.290e-01;QD=22.80;ReadPosRankSum=1.04;SOR=0.784	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,33:57:99:0|1:10102234_C_T:1307,0,2634
-20	10102363	.	A	T	1235.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.780e-01;ClippingRankSum=-1.158e+00;DP=69;ExcessHet=3.0103;FS=2.050;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-8.580e-01;QD=17.91;ReadPosRankSum=-4.200e-02;SOR=0.438	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1243,0,1226
-20	10102530	.	C	T	717.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.292;ClippingRankSum=0.380;DP=38;ExcessHet=3.0103;FS=1.463;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-6.420e-01;QD=18.88;ReadPosRankSum=0.847;SOR=0.330	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,19:38:99:0|1:10102530_C_T:725,0,1412
-20	10102531	.	A	G	717.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.072e+00;ClippingRankSum=-7.120e-01;DP=36;ExcessHet=3.0103;FS=1.480;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=-1.028e+00;QD=19.93;ReadPosRankSum=0.933;SOR=0.324	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,18:36:99:0|1:10102530_C_T:725,0,1412
-20	10102727	.	G	T	1162.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.61;ClippingRankSum=0.798;DP=68;ExcessHet=3.0103;FS=2.067;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-3.190e-01;QD=17.10;ReadPosRankSum=2.09;SOR=0.996	GT:AD:DP:GQ:PL	0/1:35,33:68:99:1170,0,1022
-20	10102904	.	C	A	1925.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.07;ClippingRankSum=0.880;DP=100;ExcessHet=3.0103;FS=1.625;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=0.236;QD=19.26;ReadPosRankSum=0.575;SOR=0.698	GT:AD:DP:GQ:PL	0/1:45,55:100:99:1933,0,1459
-20	10103110	.	G	C	1604.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.629e+00;ClippingRankSum=-3.830e-01;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQRankSum=0.025;QD=20.31;ReadPosRankSum=1.55;SOR=0.627	GT:AD:DP:GQ:PL	0/1:33,46:79:99:1612,0,1136
-20	10103301	.	C	T	932.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.94;ClippingRankSum=-2.368e+00;DP=70;ExcessHet=3.0103;FS=0.917;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=0.605;QD=13.32;ReadPosRankSum=0.797;SOR=0.562	GT:AD:DP:GQ:PL	0/1:42,28:70:99:940,0,1468
-20	10103320	.	G	C	842.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.24;ClippingRankSum=-5.500e-01;DP=61;ExcessHet=3.0103;FS=0.984;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=0.257;QD=13.81;ReadPosRankSum=0.726;SOR=0.678	GT:AD:DP:GQ:PL	0/1:36,25:61:99:850,0,1147
-20	10103333	.	G	A	936.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.51;ClippingRankSum=-9.350e-01;DP=59;ExcessHet=3.0103;FS=7.270;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-7.790e-01;QD=16.15;ReadPosRankSum=1.01;SOR=0.888	GT:AD:DP:GQ:PL	0/1:31,27:58:99:944,0,1116
-20	10103552	.	T	G	1165.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.596e+00;ClippingRankSum=-5.000e-03;DP=75;ExcessHet=3.0103;FS=9.987;MLEAC=1;MLEAF=0.500;MQ=59.10;MQRankSum=-8.850e-01;QD=15.54;ReadPosRankSum=1.72;SOR=1.723	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1173,0,1349
-20	10103680	.	G	T	1373.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.00;ClippingRankSum=-1.123e+00;DP=79;ExcessHet=3.0103;FS=1.838;MLEAC=1;MLEAF=0.500;MQ=58.64;MQRankSum=0.427;QD=17.39;ReadPosRankSum=-2.700e-01;SOR=0.864	GT:AD:DP:GQ:PL	0/1:39,40:79:99:1381,0,1262
-20	10103751	.	G	T	999.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.96;ClippingRankSum=0.790;DP=57;ExcessHet=3.0103;FS=3.657;MLEAC=1;MLEAF=0.500;MQ=59.16;MQRankSum=0.918;QD=17.54;ReadPosRankSum=1.40;SOR=0.987	GT:AD:DP:GQ:PL	0/1:28,29:57:99:1007,0,912
-20	10103828	.	T	A	1145.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.398e+00;ClippingRankSum=0.359;DP=66;ExcessHet=3.0103;FS=0.942;MLEAC=1;MLEAF=0.500;MQ=58.50;MQRankSum=0.398;QD=17.36;ReadPosRankSum=1.01;SOR=0.489	GT:AD:DP:GQ:PL	0/1:33,33:66:99:1153,0,1178
-20	10103849	.	T	C	1396.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.747e+00;ClippingRankSum=0.609;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQRankSum=0.446;QD=20.84;ReadPosRankSum=-5.600e-02;SOR=0.720	GT:AD:DP:GQ:PGT:PID:PL	0/1:32,35:67:99:0|1:10103849_T_C:1404,0,1261
-20	10103850	.	G	A	1396.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.32;ClippingRankSum=-6.310e-01;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQRankSum=1.22;QD=20.24;ReadPosRankSum=1.16;SOR=0.724	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,36:69:99:0|1:10103849_T_C:1404,0,1261
-20	10104018	.	C	T	1203.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.68;ClippingRankSum=1.01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.52;MQRankSum=1.98;QD=16.49;ReadPosRankSum=-3.700e-01;SOR=0.760	GT:AD:DP:GQ:PL	0/1:37,36:73:99:1211,0,1190
-20	10104352	.	A	G	1558.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.163e+00;ClippingRankSum=-1.032e+00;DP=87;ExcessHet=3.0103;FS=2.942;MLEAC=1;MLEAF=0.500;MQ=58.93;MQRankSum=-1.350e+00;QD=19.01;ReadPosRankSum=-7.620e-01;SOR=0.425	GT:AD:DP:GQ:PL	0/1:36,46:82:99:1566,0,1206
-20	10104593	.	G	C	780.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.346e+00;ClippingRankSum=-8.950e-01;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQRankSum=-5.130e-01;QD=12.20;ReadPosRankSum=0.294;SOR=0.784	GT:AD:DP:GQ:PL	0/1:38,26:64:99:788,0,1312
+20	10101288	.	A	G	1006.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.190e-01;ClippingRankSum=1.08;DP=68;ExcessHet=3.0103;FS=2.070;MLEAC=1;MLEAF=0.500;MQ=58.42;MQRankSum=0.517;QD=14.80;ReadPosRankSum=-1.128e+00;SOR=1.040	GT:AD:DP:GQ:PL	0/1:37,31:68:99:1014,0,1275
+20	10101674	.	TTGTG	T,TTGTGTGTGTG	1464.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.50;QD=30.31;SOR=1.002	GT:AD:DP:GQ:PL	1/2:0,22,6:35:99:1481,557,581,932,0,925
+20	10101880	.	A	G	1599.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.769e+00;ClippingRankSum=-6.570e-01;DP=84;ExcessHet=3.0103;FS=1.801;MLEAC=1;MLEAF=0.500;MQ=59.22;MQRankSum=0.207;QD=19.27;ReadPosRankSum=-1.953e+00;SOR=0.736	GT:AD:DP:GQ:PL	0/1:36,47:83:99:1607,0,1223
+20	10101912	.	C	T	1588.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=0.093;DP=86;ExcessHet=3.0103;FS=0.811;MLEAC=1;MLEAF=0.500;MQ=58.69;MQRankSum=0.569;QD=18.69;ReadPosRankSum=-4.720e-01;SOR=0.604	GT:AD:DP:GQ:PL	0/1:39,46:85:99:1596,0,1309
+20	10102234	.	C	T	1259.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.298e+00;ClippingRankSum=-5.690e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQRankSum=0.093;QD=22.90;ReadPosRankSum=0.840;SOR=0.711	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,31:55:99:0|1:10102234_C_T:1267,0,2599
+20	10102247	.	G	A	1299.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.40;ClippingRankSum=0.144;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQRankSum=0.433;QD=23.63;ReadPosRankSum=1.47;SOR=0.711	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,31:55:99:0|1:10102234_C_T:1307,0,2634
+20	10102248	.	T	C	1299.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.970e-01;ClippingRankSum=0.396;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.95;MQRankSum=-9.290e-01;QD=22.80;ReadPosRankSum=1.04;SOR=0.784	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,33:57:99:0|1:10102234_C_T:1307,0,2634
+20	10102363	.	A	T	1235.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.780e-01;ClippingRankSum=-1.158e+00;DP=69;ExcessHet=3.0103;FS=2.050;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-8.580e-01;QD=17.91;ReadPosRankSum=-4.200e-02;SOR=0.438	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1243,0,1226
+20	10102530	.	C	T	717.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.292;ClippingRankSum=0.380;DP=38;ExcessHet=3.0103;FS=1.463;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-6.420e-01;QD=18.89;ReadPosRankSum=0.847;SOR=0.330	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,19:38:99:0|1:10102530_C_T:725,0,1412
+20	10102531	.	A	G	717.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.072e+00;ClippingRankSum=-7.120e-01;DP=36;ExcessHet=3.0103;FS=1.480;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=-1.028e+00;QD=19.93;ReadPosRankSum=0.933;SOR=0.324	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,18:36:99:0|1:10102530_C_T:725,0,1412
+20	10102727	.	G	T	1162.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.61;ClippingRankSum=0.798;DP=68;ExcessHet=3.0103;FS=2.067;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-3.190e-01;QD=17.10;ReadPosRankSum=2.09;SOR=0.996	GT:AD:DP:GQ:PL	0/1:35,33:68:99:1170,0,1022
+20	10102904	.	C	A	1925.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.07;ClippingRankSum=0.880;DP=100;ExcessHet=3.0103;FS=1.625;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=0.236;QD=19.26;ReadPosRankSum=0.575;SOR=0.698	GT:AD:DP:GQ:PL	0/1:45,55:100:99:1933,0,1459
+20	10103110	.	G	C	1604.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.629e+00;ClippingRankSum=-3.830e-01;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQRankSum=0.025;QD=20.31;ReadPosRankSum=1.55;SOR=0.627	GT:AD:DP:GQ:PL	0/1:33,46:79:99:1612,0,1136
+20	10103301	.	C	T	932.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.94;ClippingRankSum=-2.368e+00;DP=70;ExcessHet=3.0103;FS=0.917;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=0.605;QD=13.32;ReadPosRankSum=0.797;SOR=0.562	GT:AD:DP:GQ:PL	0/1:42,28:70:99:940,0,1468
+20	10103320	.	G	C	842.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.24;ClippingRankSum=-5.500e-01;DP=61;ExcessHet=3.0103;FS=0.984;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=0.257;QD=13.81;ReadPosRankSum=0.726;SOR=0.678	GT:AD:DP:GQ:PL	0/1:36,25:61:99:850,0,1147
+20	10103333	.	G	A	936.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.51;ClippingRankSum=-9.350e-01;DP=59;ExcessHet=3.0103;FS=7.270;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-7.790e-01;QD=16.15;ReadPosRankSum=1.01;SOR=0.888	GT:AD:DP:GQ:PL	0/1:31,27:58:99:944,0,1116
+20	10103552	.	T	G	1165.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.596e+00;ClippingRankSum=-5.000e-03;DP=75;ExcessHet=3.0103;FS=9.987;MLEAC=1;MLEAF=0.500;MQ=59.10;MQRankSum=-8.850e-01;QD=15.54;ReadPosRankSum=1.72;SOR=1.723	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1173,0,1349
+20	10103680	.	G	T	1373.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.00;ClippingRankSum=-1.123e+00;DP=79;ExcessHet=3.0103;FS=1.838;MLEAC=1;MLEAF=0.500;MQ=58.64;MQRankSum=0.427;QD=17.39;ReadPosRankSum=-2.700e-01;SOR=0.864	GT:AD:DP:GQ:PL	0/1:39,40:79:99:1381,0,1262
+20	10103751	.	G	T	999.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.96;ClippingRankSum=0.790;DP=57;ExcessHet=3.0103;FS=3.657;MLEAC=1;MLEAF=0.500;MQ=59.16;MQRankSum=0.918;QD=17.54;ReadPosRankSum=1.40;SOR=0.987	GT:AD:DP:GQ:PL	0/1:28,29:57:99:1007,0,912
+20	10103828	.	T	A	1145.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.398e+00;ClippingRankSum=0.359;DP=66;ExcessHet=3.0103;FS=0.942;MLEAC=1;MLEAF=0.500;MQ=58.50;MQRankSum=0.398;QD=17.36;ReadPosRankSum=1.01;SOR=0.489	GT:AD:DP:GQ:PL	0/1:33,33:66:99:1153,0,1178
+20	10103849	.	T	C	1396.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.747e+00;ClippingRankSum=0.609;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQRankSum=0.446;QD=20.85;ReadPosRankSum=-5.600e-02;SOR=0.720	GT:AD:DP:GQ:PGT:PID:PL	0/1:32,35:67:99:0|1:10103849_T_C:1404,0,1261
+20	10103850	.	G	A	1396.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.32;ClippingRankSum=-6.310e-01;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQRankSum=1.22;QD=20.24;ReadPosRankSum=1.16;SOR=0.724	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,36:69:99:0|1:10103849_T_C:1404,0,1261
+20	10104018	.	C	T	1203.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.68;ClippingRankSum=1.01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.52;MQRankSum=1.98;QD=16.49;ReadPosRankSum=-3.700e-01;SOR=0.760	GT:AD:DP:GQ:PL	0/1:37,36:73:99:1211,0,1190
+20	10104352	.	A	G	1558.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.163e+00;ClippingRankSum=-1.032e+00;DP=87;ExcessHet=3.0103;FS=2.942;MLEAC=1;MLEAF=0.500;MQ=58.93;MQRankSum=-1.350e+00;QD=19.01;ReadPosRankSum=-7.620e-01;SOR=0.425	GT:AD:DP:GQ:PL	0/1:36,46:82:99:1566,0,1206
+20	10104593	.	G	C	780.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.346e+00;ClippingRankSum=-8.950e-01;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQRankSum=-5.130e-01;QD=12.20;ReadPosRankSum=0.294;SOR=0.784	GT:AD:DP:GQ:PL	0/1:38,26:64:99:788,0,1312
 20	10104648	.	AG	A	822.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.949e+00;ClippingRankSum=0.592;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-4.680e-01;QD=14.18;ReadPosRankSum=-2.634e+00;SOR=0.804	GT:AD:DP:GQ:PL	0/1:31,27:58:99:830,0,986
-20	10104694	.	T	G	1266.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;ClippingRankSum=-8.310e-01;DP=66;ExcessHet=3.0103;FS=3.646;MLEAC=1;MLEAF=0.500;MQ=59.86;MQRankSum=-3.410e-01;QD=19.19;ReadPosRankSum=0.019;SOR=0.307	GT:AD:DP:GQ:PL	0/1:30,36:66:99:1274,0,1021
+20	10104694	.	T	G	1266.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;ClippingRankSum=-8.310e-01;DP=66;ExcessHet=3.0103;FS=3.646;MLEAC=1;MLEAF=0.500;MQ=59.86;MQRankSum=-3.410e-01;QD=19.19;ReadPosRankSum=0.019;SOR=0.307	GT:AD:DP:GQ:PL	0/1:30,36:66:99:1274,0,1021
 20	10105066	.	GA	G	935.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.836e+00;ClippingRankSum=-1.198e+00;DP=47;ExcessHet=3.0103;FS=8.562;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=-2.530e-01;QD=20.34;ReadPosRankSum=0.011;SOR=1.072	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,24:46:99:0|1:10105066_GA_G:943,0,1125
-20	10105077	.	G	A	908.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=0.869;DP=44;ExcessHet=3.0103;FS=6.222;MLEAC=1;MLEAF=0.500;MQ=59.93;MQRankSum=-4.460e-01;QD=20.65;ReadPosRankSum=-6.580e-01;SOR=0.377	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,23:44:99:0|1:10105066_GA_G:916,0,1104
-20	10105095	.	A	T	782.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=0.353;DP=43;ExcessHet=3.0103;FS=15.611;MLEAC=1;MLEAF=0.500;MQ=59.93;MQRankSum=0.134;QD=18.20;ReadPosRankSum=-1.181e+00;SOR=0.056	GT:AD:DP:GQ:PL	0/1:20,23:43:99:790,0,607
-20	10105234	.	A	T	1018.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.714e+00;ClippingRankSum=-1.881e+00;DP=65;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=1.54;QD=15.92;ReadPosRankSum=0.873;SOR=0.492	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1026,0,1174
-20	10105358	.	A	G	1089.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.404e+00;ClippingRankSum=0.305;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=2.32;QD=15.35;ReadPosRankSum=1.16;SOR=0.720	GT:AD:DP:GQ:PL	0/1:34,37:71:99:1097,0,1195
-20	10106404	.	T	C	794.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;ClippingRankSum=-6.160e-01;DP=65;ExcessHet=3.0103;FS=0.996;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-3.500e-02;QD=12.61;ReadPosRankSum=1.75;SOR=0.478	GT:AD:DP:GQ:PL	0/1:39,24:63:99:802,0,1376
-20	10106429	.	C	A	1127.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=-3.570e-01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=1.93;QD=15.03;ReadPosRankSum=-1.996e+00;SOR=0.665	GT:AD:DP:GQ:PL	0/1:41,34:75:99:1135,0,1364
-20	10106802	.	G	A	1410.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.07;ClippingRankSum=0.201;DP=80;ExcessHet=3.0103;FS=2.988;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.907;QD=17.86;ReadPosRankSum=0.838;SOR=0.794	GT:AD:DP:GQ:PL	0/1:39,40:79:99:1418,0,1293
-20	10106858	.	C	G	964.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.97;ClippingRankSum=-7.350e-01;DP=68;ExcessHet=3.0103;FS=2.037;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.204;QD=14.19;ReadPosRankSum=-6.000e-03;SOR=0.670	GT:AD:DP:GQ:PL	0/1:38,30:68:99:972,0,1186
-20	10106889	.	C	T	767.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.623;ClippingRankSum=-6.230e-01;DP=52;ExcessHet=3.0103;FS=1.077;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.300e-02;QD=14.76;ReadPosRankSum=-9.160e-01;SOR=0.456	GT:AD:DP:GQ:PL	0/1:27,25:52:99:775,0,867
+20	10105077	.	G	A	908.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=0.869;DP=44;ExcessHet=3.0103;FS=6.222;MLEAC=1;MLEAF=0.500;MQ=59.93;MQRankSum=-4.460e-01;QD=20.65;ReadPosRankSum=-6.580e-01;SOR=0.377	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,23:44:99:0|1:10105066_GA_G:916,0,1104
+20	10105095	.	A	T	782.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=0.353;DP=43;ExcessHet=3.0103;FS=15.611;MLEAC=1;MLEAF=0.500;MQ=59.93;MQRankSum=0.134;QD=18.20;ReadPosRankSum=-1.181e+00;SOR=0.056	GT:AD:DP:GQ:PL	0/1:20,23:43:99:790,0,607
+20	10105234	.	A	T	1018.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.714e+00;ClippingRankSum=-1.881e+00;DP=65;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=1.54;QD=15.92;ReadPosRankSum=0.873;SOR=0.492	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1026,0,1174
+20	10105358	.	A	G	1089.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.404e+00;ClippingRankSum=0.305;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=2.32;QD=15.35;ReadPosRankSum=1.16;SOR=0.720	GT:AD:DP:GQ:PL	0/1:34,37:71:99:1097,0,1195
+20	10106404	.	T	C	794.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;ClippingRankSum=-6.160e-01;DP=65;ExcessHet=3.0103;FS=0.996;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-3.500e-02;QD=12.61;ReadPosRankSum=1.75;SOR=0.478	GT:AD:DP:GQ:PL	0/1:39,24:63:99:802,0,1376
+20	10106429	.	C	A	1127.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=-3.570e-01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=1.93;QD=15.04;ReadPosRankSum=-1.996e+00;SOR=0.665	GT:AD:DP:GQ:PL	0/1:41,34:75:99:1135,0,1364
+20	10106802	.	G	A	1410.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.07;ClippingRankSum=0.201;DP=80;ExcessHet=3.0103;FS=2.988;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.907;QD=17.86;ReadPosRankSum=0.838;SOR=0.794	GT:AD:DP:GQ:PL	0/1:39,40:79:99:1418,0,1293
+20	10106858	.	C	G	964.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.97;ClippingRankSum=-7.350e-01;DP=68;ExcessHet=3.0103;FS=2.037;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.204;QD=14.19;ReadPosRankSum=-6.000e-03;SOR=0.670	GT:AD:DP:GQ:PL	0/1:38,30:68:99:972,0,1186
+20	10106889	.	C	T	767.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.623;ClippingRankSum=-6.230e-01;DP=52;ExcessHet=3.0103;FS=1.077;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.300e-02;QD=14.76;ReadPosRankSum=-9.160e-01;SOR=0.456	GT:AD:DP:GQ:PL	0/1:27,25:52:99:775,0,867
 20	10107047	.	AG	A	1578.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-4.040e-01;DP=81;ExcessHet=3.0103;FS=5.740;MLEAC=1;MLEAF=0.500;MQ=59.98;MQRankSum=0.087;QD=19.73;ReadPosRankSum=1.45;SOR=0.311	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,41:80:99:0|1:10107047_AG_A:1586,0,2896
-20	10107052	.	C	T	1545.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.82;ClippingRankSum=-3.680e-01;DP=80;ExcessHet=3.0103;FS=5.883;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.544;QD=19.56;ReadPosRankSum=1.94;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,40:79:99:0|1:10107047_AG_A:1553,0,2899
-20	10107331	.	G	GTT	782.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.867;ClippingRankSum=-4.390e-01;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.67;MQRankSum=0.889;QD=19.09;ReadPosRankSum=-2.194e+00;SOR=0.628	GT:AD:DP:GQ:PL	0/1:18,23:46:99:790,0,498
-20	10107686	.	C	T	1522.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.51;ClippingRankSum=-1.000e-01;DP=77;ExcessHet=3.0103;FS=6.354;MLEAC=1;MLEAF=0.500;MQ=59.10;MQRankSum=-2.600e-02;QD=20.03;ReadPosRankSum=1.34;SOR=1.448	GT:AD:DP:GQ:PL	0/1:32,44:76:99:1530,0,991
-20	10108754	.	T	G	1589.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.199e+00;ClippingRankSum=-1.347e+00;DP=92;ExcessHet=3.0103;FS=3.943;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.918;QD=17.28;ReadPosRankSum=-1.199e+00;SOR=1.032	GT:AD:DP:GQ:PL	0/1:46,46:92:99:1597,0,1631
-20	10108866	.	C	T	1173.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=1.93;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.281;QD=15.65;ReadPosRankSum=0.165;SOR=0.606	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1181,0,1372
-20	10108941	.	T	C	871.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798e+00;ClippingRankSum=-5.700e-01;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-1.220e+00;QD=14.29;ReadPosRankSum=-1.856e+00;SOR=0.772	GT:AD:DP:GQ:PL	0/1:32,29:61:99:879,0,1035
-20	10109709	.	C	G	999.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.921e+00;ClippingRankSum=0.940;DP=65;ExcessHet=3.0103;FS=2.069;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.215;QD=15.62;ReadPosRankSum=0.269;SOR=0.985	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1007,0,1159
+20	10107052	.	C	T	1545.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.82;ClippingRankSum=-3.680e-01;DP=80;ExcessHet=3.0103;FS=5.883;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.544;QD=19.57;ReadPosRankSum=1.94;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,40:79:99:0|1:10107047_AG_A:1553,0,2899
+20	10107331	.	G	GTT	782.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.867;ClippingRankSum=-4.390e-01;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.67;MQRankSum=0.889;QD=19.09;ReadPosRankSum=-2.194e+00;SOR=0.628	GT:AD:DP:GQ:PL	0/1:18,23:46:99:790,0,498
+20	10107686	.	C	T	1522.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.51;ClippingRankSum=-1.000e-01;DP=77;ExcessHet=3.0103;FS=6.354;MLEAC=1;MLEAF=0.500;MQ=59.10;MQRankSum=-2.600e-02;QD=20.03;ReadPosRankSum=1.34;SOR=1.448	GT:AD:DP:GQ:PL	0/1:32,44:76:99:1530,0,991
+20	10108754	.	T	G	1589.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.199e+00;ClippingRankSum=-1.347e+00;DP=92;ExcessHet=3.0103;FS=3.943;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.918;QD=17.28;ReadPosRankSum=-1.199e+00;SOR=1.032	GT:AD:DP:GQ:PL	0/1:46,46:92:99:1597,0,1631
+20	10108866	.	C	T	1173.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=1.93;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.281;QD=15.65;ReadPosRankSum=0.165;SOR=0.606	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1181,0,1372
+20	10108941	.	T	C	871.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798e+00;ClippingRankSum=-5.700e-01;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-1.220e+00;QD=14.29;ReadPosRankSum=-1.856e+00;SOR=0.772	GT:AD:DP:GQ:PL	0/1:32,29:61:99:879,0,1035
+20	10109709	.	C	G	999.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.921e+00;ClippingRankSum=0.940;DP=65;ExcessHet=3.0103;FS=2.069;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.215;QD=15.62;ReadPosRankSum=0.269;SOR=0.985	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1007,0,1159
 20	10110726	.	GT	G	1000.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=-1.658e+00;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQRankSum=0.826;QD=14.93;ReadPosRankSum=0.334;SOR=0.653	GT:AD:DP:GQ:PL	0/1:30,37:67:99:1008,0,777
-20	10111346	.	A	G	1046.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.404e+00;ClippingRankSum=0.017;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-1.440e-01;QD=14.74;ReadPosRankSum=0.537;SOR=0.787	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1054,0,1378
-20	10111701	.	C	A	1469.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.490e-01;ClippingRankSum=-1.240e-01;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.80;QD=19.86;ReadPosRankSum=0.492;SOR=0.793	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,38:74:99:0|1:10111701_C_A:1477,0,2752
-20	10111705	.	T	A	1464.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.785e+00;ClippingRankSum=0.341;DP=74;ExcessHet=3.0103;FS=1.888;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.05;QD=19.79;ReadPosRankSum=1.62;SOR=0.935	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,36:74:99:0|1:10111701_C_A:1472,0,2785
-20	10111919	.	A	G	1760.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.34;ClippingRankSum=3.000e-03;DP=101;ExcessHet=3.0103;FS=6.421;MLEAC=1;MLEAF=0.500;MQ=59.21;MQRankSum=-9.690e-01;QD=17.61;ReadPosRankSum=-1.830e-01;SOR=0.313	GT:AD:DP:GQ:PL	0/1:48,52:100:99:1768,0,1600
-20	10112391	.	G	T	657.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280e+00;ClippingRankSum=0.733;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-5.570e-01;QD=13.15;ReadPosRankSum=-7.130e-01;SOR=0.658	GT:AD:DP:GQ:PL	0/1:28,22:50:99:665,0,931
-20	10112869	.	T	C	534.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.194e+00;ClippingRankSum=-1.200e-02;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQRankSum=-1.100e-01;QD=12.43;ReadPosRankSum=1.06;SOR=0.636	GT:AD:DP:GQ:PL	0/1:24,19:43:99:542,0,832
-20	10113407	.	T	G	83.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.771e+00;ClippingRankSum=-6.670e-01;DP=51;ExcessHet=3.0103;FS=61.081;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.376;QD=1.67;ReadPosRankSum=-2.680e+00;SOR=4.796	GT:AD:DP:GQ:PL	0/1:40,10:50:91:91,0,1396
-20	10113421	.	G	A	650.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.98;ClippingRankSum=0.271;DP=40;ExcessHet=3.0103;FS=1.618;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.352;QD=16.27;ReadPosRankSum=1.63;SOR=0.374	GT:AD:DP:GQ:PL	0/1:21,19:40:99:658,0,661
-20	10113638	.	G	C	1279.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.179e+00;ClippingRankSum=1.99;DP=73;ExcessHet=3.0103;FS=3.240;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=0.525;QD=17.77;ReadPosRankSum=0.908;SOR=1.171	GT:AD:DP:GQ:PL	0/1:34,38:72:99:1287,0,1132
-20	10114045	.	T	A	1322.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.568e+00;ClippingRankSum=0.00;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=1.40;QD=15.75;ReadPosRankSum=-2.420e-01;SOR=0.610	GT:AD:DP:GQ:PL	0/1:43,41:84:99:1330,0,1490
+20	10111346	.	A	G	1046.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.404e+00;ClippingRankSum=0.017;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-1.440e-01;QD=14.74;ReadPosRankSum=0.537;SOR=0.787	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1054,0,1378
+20	10111701	.	C	A	1469.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.490e-01;ClippingRankSum=-1.240e-01;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.80;QD=19.86;ReadPosRankSum=0.492;SOR=0.793	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,38:74:99:0|1:10111701_C_A:1477,0,2752
+20	10111705	.	T	A	1464.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.785e+00;ClippingRankSum=0.341;DP=74;ExcessHet=3.0103;FS=1.888;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.05;QD=19.79;ReadPosRankSum=1.62;SOR=0.935	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,36:74:99:0|1:10111701_C_A:1472,0,2785
+20	10111919	.	A	G	1760.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.34;ClippingRankSum=3.000e-03;DP=101;ExcessHet=3.0103;FS=6.421;MLEAC=1;MLEAF=0.500;MQ=59.21;MQRankSum=-9.690e-01;QD=17.61;ReadPosRankSum=-1.830e-01;SOR=0.313	GT:AD:DP:GQ:PL	0/1:48,52:100:99:1768,0,1600
+20	10112391	.	G	T	657.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280e+00;ClippingRankSum=0.733;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-5.570e-01;QD=13.15;ReadPosRankSum=-7.130e-01;SOR=0.658	GT:AD:DP:GQ:PL	0/1:28,22:50:99:665,0,931
+20	10112869	.	T	C	534.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.194e+00;ClippingRankSum=-1.200e-02;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQRankSum=-1.100e-01;QD=12.43;ReadPosRankSum=1.06;SOR=0.636	GT:AD:DP:GQ:PL	0/1:24,19:43:99:542,0,832
+20	10113407	.	T	G	83.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.771e+00;ClippingRankSum=-6.670e-01;DP=51;ExcessHet=3.0103;FS=61.081;MLEAC=1;MLEAF=0.500;MQ=59.55;MQRankSum=0.376;QD=1.67;ReadPosRankSum=-2.680e+00;SOR=4.796	GT:AD:DP:GQ:PL	0/1:40,10:50:91:91,0,1396
+20	10113421	.	G	A	650.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.98;ClippingRankSum=0.271;DP=40;ExcessHet=3.0103;FS=1.618;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.352;QD=16.27;ReadPosRankSum=1.63;SOR=0.374	GT:AD:DP:GQ:PL	0/1:21,19:40:99:658,0,661
+20	10113638	.	G	C	1279.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.179e+00;ClippingRankSum=1.99;DP=73;ExcessHet=3.0103;FS=3.240;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=0.525;QD=17.77;ReadPosRankSum=0.908;SOR=1.171	GT:AD:DP:GQ:PL	0/1:34,38:72:99:1287,0,1132
+20	10114045	.	T	A	1322.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.568e+00;ClippingRankSum=0.00;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=1.40;QD=15.75;ReadPosRankSum=-2.420e-01;SOR=0.610	GT:AD:DP:GQ:PL	0/1:43,41:84:99:1330,0,1490
 20	10114705	.	CA	C	527.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.81;ClippingRankSum=1.60;DP=80;ExcessHet=3.0103;FS=4.915;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.093;QD=8.12;ReadPosRankSum=-5.250e-01;SOR=1.382	GT:AD:DP:GQ:PL	0/1:38,27:68:99:535,0,870
-20	10115097	.	C	G	1216.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.281;ClippingRankSum=-5.140e-01;DP=77;ExcessHet=3.0103;FS=4.468;MLEAC=1;MLEAF=0.500;MQ=59.21;MQRankSum=1.11;QD=16.22;ReadPosRankSum=1.12;SOR=0.969	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1224,0,1348
-20	10115325	.	C	T	1181.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;ClippingRankSum=-7.820e-01;DP=77;ExcessHet=3.0103;FS=0.876;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.770e-01;QD=15.55;ReadPosRankSum=1.62;SOR=0.541	GT:AD:DP:GQ:PL	0/1:41,35:76:99:1189,0,1426
-20	10115599	.	C	A	931.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-3.320e-01;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQRankSum=-2.050e-01;QD=15.03;ReadPosRankSum=-2.383e+00;SOR=0.608	GT:AD:DP:GQ:PL	0/1:34,28:62:99:939,0,1209
-20	10119749	.	G	A	1169.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.40;ClippingRankSum=-6.510e-01;DP=93;ExcessHet=3.0103;FS=0.802;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=4.000e-03;QD=12.58;ReadPosRankSum=-8.950e-01;SOR=0.538	GT:AD:DP:GQ:PL	0/1:57,36:93:99:1177,0,1818
-20	10120207	.	C	CAGGCCACAA	1372.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073e+00;ClippingRankSum=-2.046e+00;DP=60;ExcessHet=3.0103;FS=3.570;MLEAC=1;MLEAF=0.500;MQ=46.14;MQRankSum=-6.580e+00;QD=23.27;ReadPosRankSum=-5.860e-01;SOR=1.069	GT:AD:DP:GQ:PL	0/1:27,32:59:99:1380,0,2579
-20	10120854	.	G	T	1433.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.62;ClippingRankSum=0.870;DP=74;ExcessHet=3.0103;FS=0.919;MLEAC=1;MLEAF=0.500;MQ=59.50;MQRankSum=-4.290e-01;QD=19.91;ReadPosRankSum=0.723;SOR=0.528	GT:AD:DP:GQ:PL	0/1:33,39:72:99:1441,0,924
-20	10121178	.	C	T	988.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.090e-01;ClippingRankSum=-8.990e-01;DP=69;ExcessHet=3.0103;FS=8.368;MLEAC=1;MLEAF=0.500;MQ=59.12;MQRankSum=0.682;QD=14.33;ReadPosRankSum=-1.345e+00;SOR=1.317	GT:AD:DP:GQ:PL	0/1:38,31:69:99:996,0,1321
-20	10121202	.	C	A	1225.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.596;ClippingRankSum=-1.057e+00;DP=87;ExcessHet=3.0103;FS=2.854;MLEAC=1;MLEAF=0.500;MQ=59.04;MQRankSum=0.378;QD=14.25;ReadPosRankSum=-4.650e-01;SOR=1.040	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1233,0,1707
-20	10121272	.	G	A	1350.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.910e-01;ClippingRankSum=1.35;DP=87;ExcessHet=3.0103;FS=0.810;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=0.761;QD=15.52;ReadPosRankSum=-1.280e+00;SOR=0.855	GT:AD:DP:GQ:PL	0/1:46,41:87:99:1358,0,1588
-20	10121684	.	C	T	1840.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.62;ClippingRankSum=0.990;DP=91;ExcessHet=3.0103;FS=1.716;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.782;QD=20.23;ReadPosRankSum=1.26;SOR=0.516	GT:AD:DP:GQ:PL	0/1:39,52:91:99:1848,0,1246
-20	10122275	.	A	G	1119.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.600e-02;ClippingRankSum=-7.700e-01;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQRankSum=-1.936e+00;QD=13.33;ReadPosRankSum=0.351;SOR=0.720	GT:AD:DP:GQ:PL	0/1:50,34:84:99:1127,0,1719
-20	10122669	.	G	T	788.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;ClippingRankSum=-2.900e-02;DP=62;ExcessHet=3.0103;FS=13.281;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=3.45;QD=15.77;ReadPosRankSum=1.09;SOR=1.869	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,22:50:99:0|1:10122669_G_T:796,0,1976
-20	10122672	.	A	G	788.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.683e+00;ClippingRankSum=0.050;DP=61;ExcessHet=3.0103;FS=13.703;MLEAC=1;MLEAF=0.500;MQ=56.25;MQRankSum=-1.110e-01;QD=16.09;ReadPosRankSum=0.251;SOR=1.856	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,22:49:99:0|1:10122669_G_T:796,0,1976
-20	10124075	.	G	C	1073.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.310e-01;ClippingRankSum=1.26;DP=63;ExcessHet=3.0103;FS=5.014;MLEAC=1;MLEAF=0.500;MQ=59.63;MQRankSum=0.117;QD=17.04;ReadPosRankSum=1.07;SOR=1.251	GT:AD:DP:GQ:PL	0/1:31,32:63:99:1081,0,1032
-20	10124267	.	C	T	1488.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.07;ClippingRankSum=-6.990e-01;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.930e-01;QD=18.61;ReadPosRankSum=0.371;SOR=0.675	GT:AD:DP:GQ:PL	0/1:38,42:80:99:1496,0,1121
-20	10126398	.	T	A	1653.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.71;ClippingRankSum=-2.275e+00;DP=88;ExcessHet=3.0103;FS=4.161;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=0.602;QD=19.01;ReadPosRankSum=-4.900e-02;SOR=1.228	GT:AD:DP:GQ:PL	0/1:39,48:87:99:1661,0,1257
-20	10128634	.	T	G	1200.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.447e+00;ClippingRankSum=1.07;DP=92;ExcessHet=3.0103;FS=1.802;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.35;QD=13.05;ReadPosRankSum=-5.210e-01;SOR=0.922	GT:AD:DP:GQ:PL	0/1:53,39:92:99:1208,0,1966
-20	10128652	.	T	C	4007.03	.	AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.84;SOR=1.634	GT:AD:DP:GQ:PL	1/1:0,98:98:99:4021,294,0
-20	10129396	.	A	G	1202.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.700e-02;ClippingRankSum=-2.700e-02;DP=75;ExcessHet=3.0103;FS=7.765;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-9.000e-02;QD=16.03;ReadPosRankSum=1.72;SOR=0.246	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1210,0,1385
-20	10129600	.	A	G	3446.03	.	AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;QD=28.80;SOR=0.756	GT:AD:DP:GQ:PL	1/1:0,97:97:99:3460,290,0
-20	10130017	.	G	A	3993.03	.	AC=2;AF=1.00;AN=2;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.66;QD=29.95;SOR=1.090	GT:AD:DP:GQ:PL	1/1:0,99:99:99:4007,298,0
-20	10130249	.	AACAC	A,AAC	1176.06	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-7.320e-01;ClippingRankSum=0.032;DP=58;ExcessHet=3.0103;FS=3.448;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.64;MQRankSum=-4.780e-01;QD=30.16;ReadPosRankSum=0.287;SOR=2.242	GT:AD:DP:GQ:PL	1/2:2,19,18:39:99:1193,476,600,529,0,487
-20	10130306	.	A	ATG	1161.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.317e+00;ClippingRankSum=0.052;DP=81;ExcessHet=3.0103;FS=1.153;MLEAC=1;MLEAF=0.500;MQ=52.97;MQRankSum=-3.985e+00;QD=16.36;ReadPosRankSum=1.71;SOR=0.448	GT:AD:DP:GQ:PL	0/1:35,36:71:99:1169,0,1122
-20	10130345	.	G	GTA	806.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=-2.508e+00;DP=76;ExcessHet=3.0103;FS=2.286;MLEAC=1;MLEAF=0.500;MQ=55.28;MQRankSum=-1.956e+00;QD=13.67;ReadPosRankSum=-8.210e-01;SOR=0.425	GT:AD:DP:GQ:PL	0/1:34,25:59:99:814,0,1126
-20	10130722	.	G	A	1376.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.23;ClippingRankSum=-9.620e-01;DP=74;ExcessHet=3.0103;FS=7.888;MLEAC=1;MLEAF=0.500;MQ=56.28;MQRankSum=-4.110e-01;QD=18.60;ReadPosRankSum=1.18;SOR=0.936	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,37:74:99:0|1:10130722_G_A:1384,0,2356
+20	10115097	.	C	G	1216.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.281;ClippingRankSum=-5.140e-01;DP=77;ExcessHet=3.0103;FS=4.468;MLEAC=1;MLEAF=0.500;MQ=59.21;MQRankSum=1.11;QD=16.22;ReadPosRankSum=1.12;SOR=0.969	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1224,0,1348
+20	10115325	.	C	T	1181.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;ClippingRankSum=-7.820e-01;DP=77;ExcessHet=3.0103;FS=0.876;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.770e-01;QD=15.55;ReadPosRankSum=1.62;SOR=0.541	GT:AD:DP:GQ:PL	0/1:41,35:76:99:1189,0,1426
+20	10115599	.	C	A	931.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-3.320e-01;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQRankSum=-2.050e-01;QD=15.03;ReadPosRankSum=-2.383e+00;SOR=0.608	GT:AD:DP:GQ:PL	0/1:34,28:62:99:939,0,1209
+20	10119749	.	G	A	1169.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.40;ClippingRankSum=-6.510e-01;DP=93;ExcessHet=3.0103;FS=0.802;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=4.000e-03;QD=12.58;ReadPosRankSum=-8.950e-01;SOR=0.538	GT:AD:DP:GQ:PL	0/1:57,36:93:99:1177,0,1818
+20	10120207	.	C	CAGGCCACAA	1372.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073e+00;ClippingRankSum=-2.046e+00;DP=60;ExcessHet=3.0103;FS=3.570;MLEAC=1;MLEAF=0.500;MQ=46.14;MQRankSum=-6.580e+00;QD=23.26;ReadPosRankSum=-5.860e-01;SOR=1.069	GT:AD:DP:GQ:PL	0/1:27,32:59:99:1380,0,2579
+20	10120854	.	G	T	1433.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.62;ClippingRankSum=0.870;DP=74;ExcessHet=3.0103;FS=0.919;MLEAC=1;MLEAF=0.500;MQ=59.50;MQRankSum=-4.290e-01;QD=19.91;ReadPosRankSum=0.723;SOR=0.528	GT:AD:DP:GQ:PL	0/1:33,39:72:99:1441,0,924
+20	10121178	.	C	T	988.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.090e-01;ClippingRankSum=-8.990e-01;DP=69;ExcessHet=3.0103;FS=8.368;MLEAC=1;MLEAF=0.500;MQ=59.12;MQRankSum=0.682;QD=14.33;ReadPosRankSum=-1.345e+00;SOR=1.317	GT:AD:DP:GQ:PL	0/1:38,31:69:99:996,0,1321
+20	10121202	.	C	A	1225.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.596;ClippingRankSum=-1.057e+00;DP=87;ExcessHet=3.0103;FS=2.854;MLEAC=1;MLEAF=0.500;MQ=59.04;MQRankSum=0.378;QD=14.25;ReadPosRankSum=-4.650e-01;SOR=1.040	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1233,0,1707
+20	10121272	.	G	A	1350.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.910e-01;ClippingRankSum=1.35;DP=87;ExcessHet=3.0103;FS=0.810;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=0.761;QD=15.52;ReadPosRankSum=-1.280e+00;SOR=0.855	GT:AD:DP:GQ:PL	0/1:46,41:87:99:1358,0,1588
+20	10121684	.	C	T	1840.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.62;ClippingRankSum=0.990;DP=91;ExcessHet=3.0103;FS=1.716;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.782;QD=20.23;ReadPosRankSum=1.26;SOR=0.516	GT:AD:DP:GQ:PL	0/1:39,52:91:99:1848,0,1246
+20	10122275	.	A	G	1119.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.600e-02;ClippingRankSum=-7.700e-01;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQRankSum=-1.936e+00;QD=13.33;ReadPosRankSum=0.351;SOR=0.720	GT:AD:DP:GQ:PL	0/1:50,34:84:99:1127,0,1719
+20	10122669	.	G	T	788.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;ClippingRankSum=-2.900e-02;DP=62;ExcessHet=3.0103;FS=13.281;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=3.45;QD=15.77;ReadPosRankSum=1.09;SOR=1.869	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,22:50:99:0|1:10122669_G_T:796,0,1976
+20	10122672	.	A	G	788.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.683e+00;ClippingRankSum=0.050;DP=61;ExcessHet=3.0103;FS=13.703;MLEAC=1;MLEAF=0.500;MQ=56.25;MQRankSum=-1.110e-01;QD=16.09;ReadPosRankSum=0.251;SOR=1.856	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,22:49:99:0|1:10122669_G_T:796,0,1976
+20	10124075	.	G	C	1073.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.310e-01;ClippingRankSum=1.26;DP=63;ExcessHet=3.0103;FS=5.014;MLEAC=1;MLEAF=0.500;MQ=59.63;MQRankSum=0.117;QD=17.04;ReadPosRankSum=1.07;SOR=1.251	GT:AD:DP:GQ:PL	0/1:31,32:63:99:1081,0,1032
+20	10124267	.	C	T	1488.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.07;ClippingRankSum=-6.990e-01;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.930e-01;QD=18.61;ReadPosRankSum=0.371;SOR=0.675	GT:AD:DP:GQ:PL	0/1:38,42:80:99:1496,0,1121
+20	10126398	.	T	A	1653.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.71;ClippingRankSum=-2.275e+00;DP=88;ExcessHet=3.0103;FS=4.161;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=0.602;QD=19.01;ReadPosRankSum=-4.900e-02;SOR=1.228	GT:AD:DP:GQ:PL	0/1:39,48:87:99:1661,0,1257
+20	10128634	.	T	G	1200.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.447e+00;ClippingRankSum=1.07;DP=92;ExcessHet=3.0103;FS=1.802;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.35;QD=13.05;ReadPosRankSum=-5.210e-01;SOR=0.922	GT:AD:DP:GQ:PL	0/1:53,39:92:99:1208,0,1966
+20	10128652	.	T	C	4007.06	.	AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.84;SOR=1.634	GT:AD:DP:GQ:PL	1/1:0,98:98:99:4021,294,0
+20	10129396	.	A	G	1202.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.700e-02;ClippingRankSum=-2.700e-02;DP=75;ExcessHet=3.0103;FS=7.765;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-9.000e-02;QD=16.04;ReadPosRankSum=1.72;SOR=0.246	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1210,0,1385
+20	10129600	.	A	G	3446.06	.	AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;QD=28.80;SOR=0.756	GT:AD:DP:GQ:PL	1/1:0,97:97:99:3460,290,0
+20	10130017	.	G	A	3993.06	.	AC=2;AF=1.00;AN=2;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.66;QD=29.95;SOR=1.090	GT:AD:DP:GQ:PL	1/1:0,99:99:99:4007,298,0
+20	10130249	.	AACAC	A,AAC	1176.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-7.320e-01;ClippingRankSum=0.032;DP=58;ExcessHet=3.0103;FS=3.448;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.64;MQRankSum=-4.780e-01;QD=30.15;ReadPosRankSum=0.287;SOR=2.242	GT:AD:DP:GQ:PL	1/2:2,19,18:39:99:1193,476,600,529,0,487
+20	10130306	.	A	ATG	1161.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.317e+00;ClippingRankSum=0.052;DP=81;ExcessHet=3.0103;FS=1.153;MLEAC=1;MLEAF=0.500;MQ=52.97;MQRankSum=-3.985e+00;QD=16.36;ReadPosRankSum=1.71;SOR=0.448	GT:AD:DP:GQ:PL	0/1:35,36:71:99:1169,0,1122
+20	10130345	.	G	GTA	806.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=-2.508e+00;DP=76;ExcessHet=3.0103;FS=2.286;MLEAC=1;MLEAF=0.500;MQ=55.28;MQRankSum=-1.956e+00;QD=13.67;ReadPosRankSum=-8.210e-01;SOR=0.425	GT:AD:DP:GQ:PL	0/1:34,25:59:99:814,0,1126
+20	10130722	.	G	A	1376.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.23;ClippingRankSum=-9.620e-01;DP=74;ExcessHet=3.0103;FS=7.888;MLEAC=1;MLEAF=0.500;MQ=56.28;MQRankSum=-4.110e-01;QD=18.60;ReadPosRankSum=1.18;SOR=0.936	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,37:74:99:0|1:10130722_G_A:1384,0,2356
 20	10130767	.	ATGTATG	A	1192.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.06;ClippingRankSum=-2.080e-01;DP=54;ExcessHet=3.0103;FS=15.567;MLEAC=1;MLEAF=0.500;MQ=53.57;MQRankSum=-1.648e+00;QD=22.09;ReadPosRankSum=-1.266e+00;SOR=1.559	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,29:54:99:0|1:10130722_G_A:1200,0,2326
-20	10131196	.	T	C	1681.03	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.84;QD=30.22;SOR=0.784	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1695,132,0
-20	10131980	.	T	C	2757.03	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.62;QD=29.85;SOR=0.723	GT:AD:DP:GQ:PL	1/1:0,67:67:99:2771,202,0
-20	10131998	.	G	A	1263.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;ClippingRankSum=-1.233e+00;DP=60;ExcessHet=3.0103;FS=3.609;MLEAC=1;MLEAF=0.500;MQ=56.93;MQRankSum=2.32;QD=21.06;ReadPosRankSum=-2.820e-01;SOR=1.138	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,33:60:99:0|1:10131998_G_A:1271,0,961
-20	10132023	.	T	C	1098.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.446e+00;ClippingRankSum=-7.290e-01;DP=57;ExcessHet=3.0103;FS=7.216;MLEAC=1;MLEAF=0.500;MQ=57.11;MQRankSum=0.505;QD=19.27;ReadPosRankSum=1.40;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,31:57:99:0|1:10131998_G_A:1106,0,988
-20	10132091	.	A	G	897.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.290e+00;ClippingRankSum=0.068;DP=59;ExcessHet=3.0103;FS=3.570;MLEAC=1;MLEAF=0.500;MQ=58.50;MQRankSum=1.16;QD=15.21;ReadPosRankSum=-1.600e-01;SOR=0.493	GT:AD:DP:GQ:PL	0/1:32,27:59:99:905,0,1141
+20	10131196	.	T	C	1681.06	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.84;QD=30.22;SOR=0.784	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1695,132,0
+20	10131980	.	T	C	2757.06	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.62;QD=29.85;SOR=0.723	GT:AD:DP:GQ:PL	1/1:0,67:67:99:2771,202,0
+20	10131998	.	G	A	1263.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;ClippingRankSum=-1.233e+00;DP=60;ExcessHet=3.0103;FS=3.609;MLEAC=1;MLEAF=0.500;MQ=56.93;MQRankSum=2.32;QD=21.06;ReadPosRankSum=-2.820e-01;SOR=1.138	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,33:60:99:0|1:10131998_G_A:1271,0,961
+20	10132023	.	T	C	1098.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.446e+00;ClippingRankSum=-7.290e-01;DP=57;ExcessHet=3.0103;FS=7.216;MLEAC=1;MLEAF=0.500;MQ=57.11;MQRankSum=0.505;QD=19.27;ReadPosRankSum=1.40;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,31:57:99:0|1:10131998_G_A:1106,0,988
+20	10132091	.	A	G	897.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.290e+00;ClippingRankSum=0.068;DP=59;ExcessHet=3.0103;FS=3.570;MLEAC=1;MLEAF=0.500;MQ=58.50;MQRankSum=1.16;QD=15.21;ReadPosRankSum=-1.600e-01;SOR=0.493	GT:AD:DP:GQ:PL	0/1:32,27:59:99:905,0,1141
 20	10132301	.	GACACACACAC	G	882.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=0.649;DP=55;ExcessHet=3.0103;FS=4.144;MLEAC=1;MLEAF=0.500;MQ=52.35;MQRankSum=-3.522e+00;QD=18.78;ReadPosRankSum=-1.059e+00;SOR=0.447	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,23:47:99:0|1:10132301_GACACACACAC_G:890,0,2908
-20	10132340	.	A	G	1173.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.074e+00;ClippingRankSum=1.25;DP=61;ExcessHet=3.0103;FS=0.972;MLEAC=1;MLEAF=0.500;MQ=50.05;MQRankSum=-2.912e+00;QD=19.56;ReadPosRankSum=0.080;SOR=0.554	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,32:60:99:0|1:10132301_GACACACACAC_G:1181,0,2715
-20	10132706	.	G	GAC	223.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.480e-01;ClippingRankSum=0.158;DP=56;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=50.08;MQRankSum=-4.086e+00;QD=7.21;ReadPosRankSum=2.96;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:231,0,925
-20	10132707	.	T	A	224.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.800e-01;ClippingRankSum=-1.241e+00;DP=57;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=49.30;MQRankSum=-3.724e+00;QD=7.25;ReadPosRankSum=3.00;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:232,0,924
-20	10132709	.	T	A	225.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.925;ClippingRankSum=-3.390e-01;DP=54;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=48.64;MQRankSum=-3.047e+00;QD=7.28;ReadPosRankSum=2.51;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:233,0,924
-20	10132711	.	T	A	225.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=0.609;DP=49;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=47.33;MQRankSum=-3.454e+00;QD=7.28;ReadPosRankSum=2.32;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:233,0,923
-20	10132713	.	T	A	226.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.52;ClippingRankSum=0.586;DP=47;ExcessHet=3.0103;FS=6.163;MLEAC=1;MLEAF=0.500;MQ=46.71;MQRankSum=-2.978e+00;QD=7.55;ReadPosRankSum=1.55;SOR=0.959	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,8:30:99:0|1:10132706_G_GAC:234,0,923
-20	10132715	.	T	A	229.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.310e-01;ClippingRankSum=0.737;DP=44;ExcessHet=3.0103;FS=6.994;MLEAC=1;MLEAF=0.500;MQ=46.35;MQRankSum=-3.840e+00;QD=8.20;ReadPosRankSum=1.03;SOR=0.903	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,8:28:99:0|1:10132706_G_GAC:237,0,880
-20	10132717	.	T	A	236.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.611;ClippingRankSum=-2.628e+00;DP=41;ExcessHet=3.0103;FS=6.852;MLEAC=1;MLEAF=0.500;MQ=46.65;MQRankSum=-3.797e+00;QD=8.76;ReadPosRankSum=0.451;SOR=0.916	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,8:27:99:0|1:10132706_G_GAC:244,0,796
-20	10132719	.	T	A	239.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.133;ClippingRankSum=1.30;DP=41;ExcessHet=3.0103;FS=6.852;MLEAC=1;MLEAF=0.500;MQ=47.42;MQRankSum=-3.903e+00;QD=8.87;ReadPosRankSum=-3.450e-01;SOR=0.916	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,8:27:99:0|1:10132706_G_GAC:247,0,754
+20	10132340	.	A	G	1173.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.074e+00;ClippingRankSum=1.25;DP=61;ExcessHet=3.0103;FS=0.972;MLEAC=1;MLEAF=0.500;MQ=50.05;MQRankSum=-2.912e+00;QD=19.56;ReadPosRankSum=0.080;SOR=0.554	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,32:60:99:0|1:10132301_GACACACACAC_G:1181,0,2715
+20	10132706	.	G	GAC	223.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.480e-01;ClippingRankSum=0.158;DP=56;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=50.08;MQRankSum=-4.086e+00;QD=7.21;ReadPosRankSum=2.96;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:231,0,925
+20	10132707	.	T	A	224.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.800e-01;ClippingRankSum=-1.241e+00;DP=57;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=49.30;MQRankSum=-3.724e+00;QD=7.25;ReadPosRankSum=3.00;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:232,0,924
+20	10132709	.	T	A	225.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.925;ClippingRankSum=-3.390e-01;DP=54;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=48.64;MQRankSum=-3.047e+00;QD=7.28;ReadPosRankSum=2.51;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:233,0,924
+20	10132711	.	T	A	225.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=0.609;DP=49;ExcessHet=3.0103;FS=3.846;MLEAC=1;MLEAF=0.500;MQ=47.33;MQRankSum=-3.454e+00;QD=7.28;ReadPosRankSum=2.32;SOR=0.991	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,8:31:99:0|1:10132706_G_GAC:233,0,923
+20	10132713	.	T	A	226.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.52;ClippingRankSum=0.586;DP=47;ExcessHet=3.0103;FS=6.163;MLEAC=1;MLEAF=0.500;MQ=46.71;MQRankSum=-2.978e+00;QD=7.55;ReadPosRankSum=1.55;SOR=0.959	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,8:30:99:0|1:10132706_G_GAC:234,0,923
+20	10132715	.	T	A	229.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.310e-01;ClippingRankSum=0.737;DP=44;ExcessHet=3.0103;FS=6.994;MLEAC=1;MLEAF=0.500;MQ=46.35;MQRankSum=-3.840e+00;QD=8.20;ReadPosRankSum=1.03;SOR=0.903	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,8:28:99:0|1:10132706_G_GAC:237,0,880
+20	10132717	.	T	A	236.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.611;ClippingRankSum=-2.628e+00;DP=41;ExcessHet=3.0103;FS=6.852;MLEAC=1;MLEAF=0.500;MQ=46.65;MQRankSum=-3.797e+00;QD=8.76;ReadPosRankSum=0.451;SOR=0.916	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,8:27:99:0|1:10132706_G_GAC:244,0,796
+20	10132719	.	T	A	239.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.133;ClippingRankSum=1.30;DP=41;ExcessHet=3.0103;FS=6.852;MLEAC=1;MLEAF=0.500;MQ=47.42;MQRankSum=-3.903e+00;QD=8.88;ReadPosRankSum=-3.450e-01;SOR=0.916	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,8:27:99:0|1:10132706_G_GAC:247,0,754
 20	10132722	.	CAG	C,GAG	927.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=47.76;QD=31.18;SOR=1.179	GT:AD:DP:GQ:PL	1/2:0,14,8:23:99:944,561,580,421,0,728
-20	10134410	.	AAAAGAAAG	A,AAAAG	1155.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.80;QD=28.65;SOR=1.942	GT:AD:DP:GQ:PL	1/2:0,19,10:29:99:1172,402,585,755,0,717
-20	10134479	.	A	C	1431.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190e+00;ClippingRankSum=2.98;DP=75;ExcessHet=3.0103;FS=1.108;MLEAC=1;MLEAF=0.500;MQ=56.96;MQRankSum=-2.338e+00;QD=19.09;ReadPosRankSum=-1.363e+00;SOR=0.970	GT:AD:DP:GQ:PL	0/1:36,39:75:99:1439,0,1255
-20	10144244	.	C	CA	195.10	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;ClippingRankSum=-7.370e-01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.80;MQRankSum=-5.340e-01;QD=13.01;ReadPosRankSum=1.20;SOR=0.804	GT:AD:DP:GQ:PL	0/1:8,7:28:99:174,0,175
-20	10144274	.	G	A	337.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.673e+00;ClippingRankSum=-4.910e-01;DP=85;ExcessHet=3.0103;FS=61.285;MLEAC=1;MLEAF=0.500;MQ=52.47;MQRankSum=-5.896e+00;QD=4.07;ReadPosRankSum=-2.071e+00;SOR=5.782	GT:AD:DP:GQ:PGT:PID:PL	0/1:66,17:83:99:0|1:10144274_G_A:345,0,2682
-20	10144279	.	G	A	293.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.232e+00;ClippingRankSum=0.523;DP=87;ExcessHet=3.0103;FS=51.800;MLEAC=1;MLEAF=0.500;MQ=53.13;MQRankSum=-6.020e+00;QD=3.45;ReadPosRankSum=-2.884e+00;SOR=5.668	GT:AD:DP:GQ:PGT:PID:PL	0/1:69,16:85:99:0|1:10144274_G_A:301,0,2862
-20	10144284	.	C	A	467.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.442e+00;ClippingRankSum=0.274;DP=82;ExcessHet=3.0103;FS=61.606;MLEAC=1;MLEAF=0.500;MQ=55.32;MQRankSum=-3.826e+00;QD=5.70;ReadPosRankSum=-2.709e+00;SOR=5.890	GT:AD:DP:GQ:PL	0/1:64,18:82:99:475,0,2009
-20	10154221	.	C	CAGTCCTCCA	849.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.12;ClippingRankSum=0.410;DP=54;ExcessHet=3.0103;FS=6.741;MLEAC=1;MLEAF=0.500;MQ=54.60;MQRankSum=-2.981e+00;QD=18.47;ReadPosRankSum=-1.138e+00;SOR=0.379	GT:AD:DP:GQ:PL	0/1:29,17:46:99:857,0,1335
-20	10155038	.	A	AT	2573.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.27;QD=33.42;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2587,232,0
-20	10155043	.	C	CT	2234.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.30;QD=31.03;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2248,219,0
-20	10155105	.	G	A	1763.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=1.31;DP=81;ExcessHet=3.0103;FS=0.865;MLEAC=1;MLEAF=0.500;MQ=58.55;MQRankSum=-9.860e-01;QD=21.77;ReadPosRankSum=0.724;SOR=0.527	GT:AD:DP:GQ:PL	0/1:31,50:81:99:1771,0,991
-20	10156378	.	A	AT	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.850e-01;ClippingRankSum=-1.900e-02;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=-1.159e+00;QD=3.86;ReadPosRankSum=0.218;SOR=0.807	GT:AD:DP:GQ:PL	0/1:14,10:32:99:100,0,285
-20	10157869	.	GAA	G,GA	1905.06	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.102e+00;ClippingRankSum=0.262;DP=75;ExcessHet=3.0103;FS=4.393;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.29;MQRankSum=0.892;QD=28.86;ReadPosRankSum=1.05;SOR=1.241	GT:AD:DP:GQ:PL	1/2:1,33,32:66:99:1922,773,738,889,0,731
-20	10158589	.	A	AAG	1117.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.25;ClippingRankSum=-4.470e-01;DP=74;ExcessHet=3.0103;FS=4.715;MLEAC=1;MLEAF=0.500;MQ=60.42;MQRankSum=-6.940e-01;QD=15.97;ReadPosRankSum=-1.165e+00;SOR=0.639	GT:AD:DP:GQ:PL	0/1:37,33:70:99:1125,0,1291
-20	10159081	.	A	G	1672.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.992e+00;ClippingRankSum=-1.234e+00;DP=80;ExcessHet=3.0103;FS=7.829;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.280e-01;QD=20.91;ReadPosRankSum=-1.185e+00;SOR=1.262	GT:AD:DP:GQ:PL	0/1:31,49:80:99:1680,0,1033
-20	10159214	.	A	G	1026.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=-3.000e-02;DP=70;ExcessHet=3.0103;FS=19.046;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-2.670e-01;QD=14.67;ReadPosRankSum=0.587;SOR=0.576	GT:AD:DP:GQ:PL	0/1:40,30:70:99:1034,0,1274
-20	10160092	.	A	G	989.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.293e+00;ClippingRankSum=0.107;DP=50;ExcessHet=3.0103;FS=1.112;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.479;QD=19.79;ReadPosRankSum=1.34;SOR=0.925	GT:AD:DP:GQ:PL	0/1:22,28:50:99:997,0,790
-20	10160773	.	A	AC	1026.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.693;ClippingRankSum=1.41;DP=74;ExcessHet=3.0103;FS=4.863;MLEAC=1;MLEAF=0.500;MQ=60.29;MQRankSum=-1.195e+00;QD=13.87;ReadPosRankSum=0.016;SOR=0.307	GT:AD:DP:GQ:PL	0/1:42,32:74:99:1034,0,1409
-20	10161225	.	C	T	998.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.88;ClippingRankSum=-1.169e+00;DP=64;ExcessHet=3.0103;FS=3.553;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=0.629;QD=15.85;ReadPosRankSum=1.43;SOR=1.201	GT:AD:DP:GQ:PL	0/1:35,28:63:99:1006,0,1177
+20	10134410	.	AAAAGAAAG	A,AAAAG	1155.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.80;QD=28.65;SOR=1.942	GT:AD:DP:GQ:PL	1/2:0,19,10:29:99:1172,402,585,755,0,717
+20	10134479	.	A	C	1431.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190e+00;ClippingRankSum=2.98;DP=75;ExcessHet=3.0103;FS=1.108;MLEAC=1;MLEAF=0.500;MQ=56.96;MQRankSum=-2.338e+00;QD=19.09;ReadPosRankSum=-1.363e+00;SOR=0.970	GT:AD:DP:GQ:PL	0/1:36,39:75:99:1439,0,1255
+20	10144244	.	C	CA	195.02	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;ClippingRankSum=-7.370e-01;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.80;MQRankSum=-5.340e-01;QD=13.00;ReadPosRankSum=1.20;SOR=0.804	GT:AD:DP:GQ:PL	0/1:8,7:28:99:174,0,175
+20	10144274	.	G	A	337.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.673e+00;ClippingRankSum=-4.910e-01;DP=85;ExcessHet=3.0103;FS=61.285;MLEAC=1;MLEAF=0.500;MQ=52.47;MQRankSum=-5.896e+00;QD=4.07;ReadPosRankSum=-2.071e+00;SOR=5.782	GT:AD:DP:GQ:PGT:PID:PL	0/1:66,17:83:99:0|1:10144274_G_A:345,0,2682
+20	10144279	.	G	A	293.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.232e+00;ClippingRankSum=0.523;DP=87;ExcessHet=3.0103;FS=51.800;MLEAC=1;MLEAF=0.500;MQ=53.13;MQRankSum=-6.020e+00;QD=3.45;ReadPosRankSum=-2.884e+00;SOR=5.668	GT:AD:DP:GQ:PGT:PID:PL	0/1:69,16:85:99:0|1:10144274_G_A:301,0,2862
+20	10144284	.	C	A	467.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.442e+00;ClippingRankSum=0.274;DP=82;ExcessHet=3.0103;FS=61.606;MLEAC=1;MLEAF=0.500;MQ=55.32;MQRankSum=-3.826e+00;QD=5.70;ReadPosRankSum=-2.709e+00;SOR=5.890	GT:AD:DP:GQ:PL	0/1:64,18:82:99:475,0,2009
+20	10154221	.	C	CAGTCCTCCA	849.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.12;ClippingRankSum=0.410;DP=54;ExcessHet=3.0103;FS=6.741;MLEAC=1;MLEAF=0.500;MQ=54.60;MQRankSum=-2.981e+00;QD=18.47;ReadPosRankSum=-1.138e+00;SOR=0.379	GT:AD:DP:GQ:PL	0/1:29,17:46:99:857,0,1335
+20	10155038	.	A	AT	2573.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.27;QD=33.42;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2587,232,0
+20	10155043	.	C	CT	2234.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.30;QD=31.03;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2248,219,0
+20	10155105	.	G	A	1763.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=1.31;DP=81;ExcessHet=3.0103;FS=0.865;MLEAC=1;MLEAF=0.500;MQ=58.55;MQRankSum=-9.860e-01;QD=21.77;ReadPosRankSum=0.724;SOR=0.527	GT:AD:DP:GQ:PL	0/1:31,50:81:99:1771,0,991
+20	10156378	.	A	AT	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.850e-01;ClippingRankSum=-1.900e-02;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=-1.159e+00;QD=3.86;ReadPosRankSum=0.218;SOR=0.807	GT:AD:DP:GQ:PL	0/1:14,10:32:99:100,0,285
+20	10157869	.	GAA	G,GA	1905.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.102e+00;ClippingRankSum=0.262;DP=75;ExcessHet=3.0103;FS=4.393;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.29;MQRankSum=0.892;QD=28.86;ReadPosRankSum=1.05;SOR=1.241	GT:AD:DP:GQ:PL	1/2:1,33,32:66:99:1922,773,738,889,0,731
+20	10158589	.	A	AAG	1117.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.25;ClippingRankSum=-4.470e-01;DP=74;ExcessHet=3.0103;FS=4.715;MLEAC=1;MLEAF=0.500;MQ=60.42;MQRankSum=-6.940e-01;QD=15.97;ReadPosRankSum=-1.165e+00;SOR=0.639	GT:AD:DP:GQ:PL	0/1:37,33:70:99:1125,0,1291
+20	10159081	.	A	G	1672.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.992e+00;ClippingRankSum=-1.234e+00;DP=80;ExcessHet=3.0103;FS=7.829;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.280e-01;QD=20.91;ReadPosRankSum=-1.185e+00;SOR=1.262	GT:AD:DP:GQ:PL	0/1:31,49:80:99:1680,0,1033
+20	10159214	.	A	G	1026.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=-3.000e-02;DP=70;ExcessHet=3.0103;FS=19.046;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-2.670e-01;QD=14.67;ReadPosRankSum=0.587;SOR=0.576	GT:AD:DP:GQ:PL	0/1:40,30:70:99:1034,0,1274
+20	10160092	.	A	G	989.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.293e+00;ClippingRankSum=0.107;DP=50;ExcessHet=3.0103;FS=1.112;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.479;QD=19.79;ReadPosRankSum=1.34;SOR=0.925	GT:AD:DP:GQ:PL	0/1:22,28:50:99:997,0,790
+20	10160773	.	A	AC	1026.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.693;ClippingRankSum=1.41;DP=74;ExcessHet=3.0103;FS=4.863;MLEAC=1;MLEAF=0.500;MQ=60.29;MQRankSum=-1.195e+00;QD=13.87;ReadPosRankSum=0.016;SOR=0.307	GT:AD:DP:GQ:PL	0/1:42,32:74:99:1034,0,1409
+20	10161225	.	C	T	998.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.88;ClippingRankSum=-1.169e+00;DP=64;ExcessHet=3.0103;FS=3.553;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=0.629;QD=15.85;ReadPosRankSum=1.43;SOR=1.201	GT:AD:DP:GQ:PL	0/1:35,28:63:99:1006,0,1177
 20	10163182	.	TA	T	268.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.527e+00;ClippingRankSum=0.029;DP=66;ExcessHet=3.0103;FS=9.536;MLEAC=1;MLEAF=0.500;MQ=57.90;MQRankSum=1.53;QD=7.07;ReadPosRankSum=3.99;SOR=1.665	GT:AD:DP:GQ:PL	0/1:21,17:38:99:276,0,378
-20	10165727	.	G	T	968.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.75;ClippingRankSum=0.657;DP=61;ExcessHet=3.0103;FS=0.974;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.58;QD=15.88;ReadPosRankSum=2.13;SOR=0.544	GT:AD:DP:GQ:PL	0/1:32,29:61:99:976,0,976
-20	10165933	.	A	G	1906.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.002e+00;ClippingRankSum=-8.970e-01;DP=90;ExcessHet=3.0103;FS=2.985;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=-3.100e-02;QD=21.91;ReadPosRankSum=-4.680e-01;SOR=1.141	GT:AD:DP:GQ:PL	0/1:33,54:87:99:1914,0,1107
-20	10166398	.	C	A	1564.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.99;ClippingRankSum=-7.350e-01;DP=89;ExcessHet=3.0103;FS=0.793;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=-1.466e+00;QD=17.58;ReadPosRankSum=0.078;SOR=0.823	GT:AD:DP:GQ:PL	0/1:43,46:89:99:1572,0,1374
-20	10168981	.	A	G	857.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.354e+00;ClippingRankSum=0.067;DP=52;ExcessHet=3.0103;FS=1.118;MLEAC=1;MLEAF=0.500;MQ=57.83;MQRankSum=-3.540e-01;QD=16.82;ReadPosRankSum=2.29;SOR=0.972	GT:AD:DP:GQ:PL	0/1:21,30:51:99:865,0,689
-20	10169643	.	C	G	1474.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.69;ClippingRankSum=0.071;DP=69;ExcessHet=3.0103;FS=5.011;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=6.000e-03;QD=22.01;ReadPosRankSum=0.564;SOR=0.307	GT:AD:DP:GQ:PL	0/1:25,42:67:99:1482,0,639
-20	10170201	.	C	T	1695.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.78;ClippingRankSum=-6.900e-02;DP=84;ExcessHet=3.0103;FS=2.020;MLEAC=1;MLEAF=0.500;MQ=59.45;MQRankSum=-6.000e-01;QD=20.43;ReadPosRankSum=1.20;SOR=1.034	GT:AD:DP:GQ:PL	0/1:37,46:83:99:1703,0,1059
-20	10170614	.	G	A	1262.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.229e+00;ClippingRankSum=2.13;DP=83;ExcessHet=3.0103;FS=1.994;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=0.580;QD=15.21;ReadPosRankSum=0.964;SOR=1.048	GT:AD:DP:GQ:PL	0/1:45,38:83:99:1270,0,1522
-20	10171007	.	C	T	1263.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.06;ClippingRankSum=1.43;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-4.000e-02;QD=16.20;ReadPosRankSum=1.87;SOR=0.617	GT:AD:DP:GQ:PL	0/1:41,37:78:99:1271,0,1344
-20	10171309	.	T	A	1236.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.769e+00;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-7.810e-01;QD=17.67;ReadPosRankSum=-3.350e-01;SOR=0.693	GT:AD:DP:GQ:PL	0/1:34,36:70:99:1244,0,1178
-20	10171737	.	G	A	1241.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.65;ClippingRankSum=0.621;DP=59;ExcessHet=3.0103;FS=9.495;MLEAC=1;MLEAF=0.500;MQ=59.61;MQRankSum=-1.557e+00;QD=21.04;ReadPosRankSum=0.575;SOR=0.163	GT:AD:DP:GQ:PL	0/1:25,34:59:99:1249,0,844
+20	10165727	.	G	T	968.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.75;ClippingRankSum=0.657;DP=61;ExcessHet=3.0103;FS=0.974;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.58;QD=15.88;ReadPosRankSum=2.13;SOR=0.544	GT:AD:DP:GQ:PL	0/1:32,29:61:99:976,0,976
+20	10165933	.	A	G	1906.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.002e+00;ClippingRankSum=-8.970e-01;DP=90;ExcessHet=3.0103;FS=2.985;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=-3.100e-02;QD=21.92;ReadPosRankSum=-4.680e-01;SOR=1.141	GT:AD:DP:GQ:PL	0/1:33,54:87:99:1914,0,1107
+20	10166398	.	C	A	1564.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.99;ClippingRankSum=-7.350e-01;DP=89;ExcessHet=3.0103;FS=0.793;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=-1.466e+00;QD=17.58;ReadPosRankSum=0.078;SOR=0.823	GT:AD:DP:GQ:PL	0/1:43,46:89:99:1572,0,1374
+20	10168981	.	A	G	857.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.354e+00;ClippingRankSum=0.067;DP=52;ExcessHet=3.0103;FS=1.118;MLEAC=1;MLEAF=0.500;MQ=57.83;MQRankSum=-3.540e-01;QD=16.82;ReadPosRankSum=2.29;SOR=0.972	GT:AD:DP:GQ:PL	0/1:21,30:51:99:865,0,689
+20	10169643	.	C	G	1474.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.69;ClippingRankSum=0.071;DP=69;ExcessHet=3.0103;FS=5.011;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=6.000e-03;QD=22.01;ReadPosRankSum=0.564;SOR=0.307	GT:AD:DP:GQ:PL	0/1:25,42:67:99:1482,0,639
+20	10170201	.	C	T	1695.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.78;ClippingRankSum=-6.900e-02;DP=84;ExcessHet=3.0103;FS=2.020;MLEAC=1;MLEAF=0.500;MQ=59.45;MQRankSum=-6.000e-01;QD=20.43;ReadPosRankSum=1.20;SOR=1.034	GT:AD:DP:GQ:PL	0/1:37,46:83:99:1703,0,1059
+20	10170614	.	G	A	1262.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.229e+00;ClippingRankSum=2.13;DP=83;ExcessHet=3.0103;FS=1.994;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=0.580;QD=15.21;ReadPosRankSum=0.964;SOR=1.048	GT:AD:DP:GQ:PL	0/1:45,38:83:99:1270,0,1522
+20	10171007	.	C	T	1263.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.06;ClippingRankSum=1.43;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=-4.000e-02;QD=16.20;ReadPosRankSum=1.87;SOR=0.617	GT:AD:DP:GQ:PL	0/1:41,37:78:99:1271,0,1344
+20	10171309	.	T	A	1236.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.769e+00;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-7.810e-01;QD=17.67;ReadPosRankSum=-3.350e-01;SOR=0.693	GT:AD:DP:GQ:PL	0/1:34,36:70:99:1244,0,1178
+20	10171737	.	G	A	1241.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.65;ClippingRankSum=0.621;DP=59;ExcessHet=3.0103;FS=9.495;MLEAC=1;MLEAF=0.500;MQ=59.61;MQRankSum=-1.557e+00;QD=21.04;ReadPosRankSum=0.575;SOR=0.163	GT:AD:DP:GQ:PL	0/1:25,34:59:99:1249,0,844
 20	10171808	.	AG	A	1291.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.134e+00;ClippingRankSum=-6.050e-01;DP=79;ExcessHet=3.0103;FS=0.882;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-5.750e-01;QD=16.56;ReadPosRankSum=-9.530e-01;SOR=0.836	GT:AD:DP:GQ:PL	0/1:40,38:78:99:1299,0,1372
-20	10172605	.	T	C	1068.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-1.256e+00;DP=77;ExcessHet=3.0103;FS=0.881;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-1.290e-01;QD=13.88;ReadPosRankSum=1.54;SOR=0.527	GT:AD:DP:GQ:PL	0/1:45,32:77:99:1076,0,1615
-20	10172676	.	C	T	1246.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.21;ClippingRankSum=1.42;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.720e-01;QD=18.33;ReadPosRankSum=0.896;SOR=0.690	GT:AD:DP:GQ:PL	0/1:33,35:68:99:1254,0,1089
-20	10172796	.	G	A	1347.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.326;ClippingRankSum=0.449;DP=82;ExcessHet=3.0103;FS=5.698;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-4.300e-02;QD=16.64;ReadPosRankSum=1.48;SOR=0.877	GT:AD:DP:GQ:PL	0/1:41,40:81:99:1355,0,1394
-20	10173177	.	G	A	979.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.72;ClippingRankSum=1.09;DP=70;ExcessHet=3.0103;FS=8.472;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-7.600e-01;QD=14.41;ReadPosRankSum=0.191;SOR=0.700	GT:AD:DP:GQ:PL	0/1:38,30:68:99:987,0,1069
-20	10174920	.	C	T	1528.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.03;ClippingRankSum=0.369;DP=92;ExcessHet=3.0103;FS=14.384;MLEAC=1;MLEAF=0.500;MQ=58.48;MQRankSum=0.520;QD=16.80;ReadPosRankSum=-1.200e-02;SOR=0.929	GT:AD:DP:GQ:PL	0/1:46,45:91:99:1536,0,1541
-20	10175125	.	T	C	1070.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.147e+00;ClippingRankSum=-1.083e+00;DP=75;ExcessHet=3.0103;FS=1.940;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.592;QD=14.27;ReadPosRankSum=1.50;SOR=0.430	GT:AD:DP:GQ:PL	0/1:42,33:75:99:1078,0,1567
+20	10172605	.	T	C	1068.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-1.256e+00;DP=77;ExcessHet=3.0103;FS=0.881;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-1.290e-01;QD=13.88;ReadPosRankSum=1.54;SOR=0.527	GT:AD:DP:GQ:PL	0/1:45,32:77:99:1076,0,1615
+20	10172676	.	C	T	1246.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.21;ClippingRankSum=1.42;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.720e-01;QD=18.33;ReadPosRankSum=0.896;SOR=0.690	GT:AD:DP:GQ:PL	0/1:33,35:68:99:1254,0,1089
+20	10172796	.	G	A	1347.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.326;ClippingRankSum=0.449;DP=82;ExcessHet=3.0103;FS=5.698;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-4.300e-02;QD=16.64;ReadPosRankSum=1.48;SOR=0.877	GT:AD:DP:GQ:PL	0/1:41,40:81:99:1355,0,1394
+20	10173177	.	G	A	979.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.72;ClippingRankSum=1.09;DP=70;ExcessHet=3.0103;FS=8.472;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-7.600e-01;QD=14.41;ReadPosRankSum=0.191;SOR=0.700	GT:AD:DP:GQ:PL	0/1:38,30:68:99:987,0,1069
+20	10174920	.	C	T	1528.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.03;ClippingRankSum=0.369;DP=92;ExcessHet=3.0103;FS=14.384;MLEAC=1;MLEAF=0.500;MQ=58.48;MQRankSum=0.520;QD=16.80;ReadPosRankSum=-1.200e-02;SOR=0.929	GT:AD:DP:GQ:PL	0/1:46,45:91:99:1536,0,1541
+20	10175125	.	T	C	1070.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.147e+00;ClippingRankSum=-1.083e+00;DP=75;ExcessHet=3.0103;FS=1.940;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.592;QD=14.28;ReadPosRankSum=1.50;SOR=0.430	GT:AD:DP:GQ:PL	0/1:42,33:75:99:1078,0,1567
 20	10175308	.	AT	A	106.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.701;ClippingRankSum=-1.800e-01;DP=63;ExcessHet=3.0103;FS=1.440;MLEAC=1;MLEAF=0.500;MQ=58.40;MQRankSum=0.741;QD=4.63;ReadPosRankSum=0.300;SOR=0.446	GT:AD:DP:GQ:PL	0/1:13,10:31:99:114,0,425
-20	10175465	.	C	G	865.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.931e+00;ClippingRankSum=-8.060e-01;DP=60;ExcessHet=3.0103;FS=1.032;MLEAC=1;MLEAF=0.500;MQ=58.99;MQRankSum=0.046;QD=14.43;ReadPosRankSum=-3.040e-01;SOR=0.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,23:60:99:0|1:10175465_C_G:873,0,3807
-20	10175474	.	A	C	972.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.006e+00;ClippingRankSum=1.19;DP=62;ExcessHet=3.0103;FS=3.512;MLEAC=1;MLEAF=0.500;MQ=58.64;MQRankSum=1.09;QD=15.69;ReadPosRankSum=-2.118e+00;SOR=0.374	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,26:62:99:0|1:10175465_C_G:980,0,3795
-20	10175495	.	A	G	1213.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.923e+00;ClippingRankSum=2.71;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQRankSum=-9.280e-01;QD=17.34;ReadPosRankSum=-6.700e-01;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:35,35:70:99:0|1:10175465_C_G:1221,0,3635
-20	10177651	.	A	G	815.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.107e+00;ClippingRankSum=0.279;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.318;QD=12.36;ReadPosRankSum=1.43;SOR=0.660	GT:AD:DP:GQ:PL	0/1:38,28:66:99:823,0,1246
-20	10177716	.	T	G	74.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.868e+00;ClippingRankSum=-1.168e+00;DP=54;ExcessHet=3.0103;FS=49.079;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=-1.960e-01;QD=1.41;ReadPosRankSum=-2.181e+00;SOR=5.279	GT:AD:DP:GQ:PL	0/1:40,13:53:82:82,0,1352
-20	10178022	.	G	T	1595.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.30;ClippingRankSum=1.46;DP=80;ExcessHet=3.0103;FS=2.011;MLEAC=1;MLEAF=0.500;MQ=58.84;MQRankSum=-4.760e-01;QD=20.99;ReadPosRankSum=0.994;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,45:76:99:1603,0,859
-20	10178187	.	C	A	1154.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.59;ClippingRankSum=-1.250e-01;DP=67;ExcessHet=3.0103;FS=8.660;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=0.820;QD=17.76;ReadPosRankSum=-7.000e-03;SOR=1.496	GT:AD:DP:GQ:PL	0/1:32,33:65:99:1162,0,1028
-20	10179531	.	G	A	1870.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.93;ClippingRankSum=-8.200e-02;DP=84;ExcessHet=3.0103;FS=0.843;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-1.218e+00;QD=22.27;ReadPosRankSum=1.86;SOR=0.764	GT:AD:DP:GQ:PL	0/1:33,51:84:99:1878,0,1074
-20	10180270	.	G	A	1198.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.36;ClippingRankSum=2.09;DP=82;ExcessHet=3.0103;FS=2.970;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-2.610e-01;QD=14.80;ReadPosRankSum=-4.610e-01;SOR=0.833	GT:AD:DP:GQ:PL	0/1:45,36:81:99:1206,0,1538
+20	10175465	.	C	G	865.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.931e+00;ClippingRankSum=-8.060e-01;DP=60;ExcessHet=3.0103;FS=1.032;MLEAC=1;MLEAF=0.500;MQ=58.99;MQRankSum=0.046;QD=14.43;ReadPosRankSum=-3.040e-01;SOR=0.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,23:60:99:0|1:10175465_C_G:873,0,3807
+20	10175474	.	A	C	972.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.006e+00;ClippingRankSum=1.19;DP=62;ExcessHet=3.0103;FS=3.512;MLEAC=1;MLEAF=0.500;MQ=58.64;MQRankSum=1.09;QD=15.69;ReadPosRankSum=-2.118e+00;SOR=0.374	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,26:62:99:0|1:10175465_C_G:980,0,3795
+20	10175495	.	A	G	1213.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.923e+00;ClippingRankSum=2.71;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQRankSum=-9.280e-01;QD=17.34;ReadPosRankSum=-6.700e-01;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:35,35:70:99:0|1:10175465_C_G:1221,0,3635
+20	10177651	.	A	G	815.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.107e+00;ClippingRankSum=0.279;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.318;QD=12.36;ReadPosRankSum=1.43;SOR=0.660	GT:AD:DP:GQ:PL	0/1:38,28:66:99:823,0,1246
+20	10177716	.	T	G	74.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.868e+00;ClippingRankSum=-1.168e+00;DP=54;ExcessHet=3.0103;FS=49.079;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=-1.960e-01;QD=1.41;ReadPosRankSum=-2.181e+00;SOR=5.279	GT:AD:DP:GQ:PL	0/1:40,13:53:82:82,0,1352
+20	10178022	.	G	T	1595.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.30;ClippingRankSum=1.46;DP=80;ExcessHet=3.0103;FS=2.011;MLEAC=1;MLEAF=0.500;MQ=58.84;MQRankSum=-4.760e-01;QD=21.00;ReadPosRankSum=0.994;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,45:76:99:1603,0,859
+20	10178187	.	C	A	1154.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.59;ClippingRankSum=-1.250e-01;DP=67;ExcessHet=3.0103;FS=8.660;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=0.820;QD=17.76;ReadPosRankSum=-7.000e-03;SOR=1.496	GT:AD:DP:GQ:PL	0/1:32,33:65:99:1162,0,1028
+20	10179531	.	G	A	1870.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.93;ClippingRankSum=-8.200e-02;DP=84;ExcessHet=3.0103;FS=0.843;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-1.218e+00;QD=22.27;ReadPosRankSum=1.86;SOR=0.764	GT:AD:DP:GQ:PL	0/1:33,51:84:99:1878,0,1074
+20	10180270	.	G	A	1198.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.36;ClippingRankSum=2.09;DP=82;ExcessHet=3.0103;FS=2.970;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-2.610e-01;QD=14.80;ReadPosRankSum=-4.610e-01;SOR=0.833	GT:AD:DP:GQ:PL	0/1:45,36:81:99:1206,0,1538
 20	10180886	.	GA	G	272.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.996;ClippingRankSum=-8.330e-01;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.16;MQRankSum=0.305;QD=10.48;ReadPosRankSum=-5.280e-01;SOR=0.874	GT:AD:DP:GQ:PL	0/1:10,16:32:99:280,0,285
-20	10181438	.	G	A	2192.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.41;ClippingRankSum=-1.080e-01;DP=117;ExcessHet=3.0103;FS=3.400;MLEAC=1;MLEAF=0.500;MQ=59.25;MQRankSum=-1.586e+00;QD=18.90;ReadPosRankSum=-3.740e-01;SOR=0.439	GT:AD:DP:GQ:PL	0/1:54,62:116:99:2200,0,1592
-20	10181582	.	C	T	1163.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=-1.355e+00;DP=78;ExcessHet=3.0103;FS=3.083;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-3.980e-01;QD=14.92;ReadPosRankSum=1.58;SOR=1.123	GT:AD:DP:GQ:PL	0/1:44,34:78:99:1171,0,1516
-20	10182254	.	T	A	1835.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=-9.300e-02;DP=88;ExcessHet=3.0103;FS=4.142;MLEAC=1;MLEAF=0.500;MQ=59.58;MQRankSum=-1.860e-01;QD=20.86;ReadPosRankSum=3.03;SOR=0.352	GT:AD:DP:GQ:PL	0/1:37,51:88:99:1843,0,1185
-20	10183018	.	T	A	1048.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.001e+00;ClippingRankSum=0.305;DP=74;ExcessHet=3.0103;FS=6.101;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.830e-01;QD=14.36;ReadPosRankSum=0.815;SOR=0.627	GT:AD:DP:GQ:PL	0/1:40,33:73:99:1056,0,1384
-20	10183517	.	A	G	1137.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.270e+00;ClippingRankSum=1.39;DP=66;ExcessHet=3.0103;FS=5.038;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-1.035e+00;QD=17.78;ReadPosRankSum=7.000e-03;SOR=1.137	GT:AD:DP:GQ:PL	0/1:28,36:64:99:1145,0,967
-20	10183783	.	C	G	1407.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.43;ClippingRankSum=0.650;DP=77;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=58.66;MQRankSum=-1.253e+00;QD=18.28;ReadPosRankSum=1.18;SOR=0.830	GT:AD:DP:GQ:PL	0/1:35,42:77:99:1415,0,1056
+20	10181438	.	G	A	2192.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.41;ClippingRankSum=-1.080e-01;DP=117;ExcessHet=3.0103;FS=3.400;MLEAC=1;MLEAF=0.500;MQ=59.25;MQRankSum=-1.586e+00;QD=18.90;ReadPosRankSum=-3.740e-01;SOR=0.439	GT:AD:DP:GQ:PL	0/1:54,62:116:99:2200,0,1592
+20	10181582	.	C	T	1163.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=-1.355e+00;DP=78;ExcessHet=3.0103;FS=3.083;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-3.980e-01;QD=14.92;ReadPosRankSum=1.58;SOR=1.123	GT:AD:DP:GQ:PL	0/1:44,34:78:99:1171,0,1516
+20	10182254	.	T	A	1835.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=-9.300e-02;DP=88;ExcessHet=3.0103;FS=4.142;MLEAC=1;MLEAF=0.500;MQ=59.58;MQRankSum=-1.860e-01;QD=20.86;ReadPosRankSum=3.03;SOR=0.352	GT:AD:DP:GQ:PL	0/1:37,51:88:99:1843,0,1185
+20	10183018	.	T	A	1048.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.001e+00;ClippingRankSum=0.305;DP=74;ExcessHet=3.0103;FS=6.101;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.830e-01;QD=14.36;ReadPosRankSum=0.815;SOR=0.627	GT:AD:DP:GQ:PL	0/1:40,33:73:99:1056,0,1384
+20	10183517	.	A	G	1137.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.270e+00;ClippingRankSum=1.39;DP=66;ExcessHet=3.0103;FS=5.038;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-1.035e+00;QD=17.78;ReadPosRankSum=7.000e-03;SOR=1.137	GT:AD:DP:GQ:PL	0/1:28,36:64:99:1145,0,967
+20	10183783	.	C	G	1407.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.43;ClippingRankSum=0.650;DP=77;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=58.66;MQRankSum=-1.253e+00;QD=18.28;ReadPosRankSum=1.18;SOR=0.830	GT:AD:DP:GQ:PL	0/1:35,42:77:99:1415,0,1056
 20	10184381	.	TCA	T	1176.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.457;ClippingRankSum=0.013;DP=68;ExcessHet=3.0103;FS=8.414;MLEAC=1;MLEAF=0.500;MQ=58.87;MQRankSum=0.793;QD=18.38;ReadPosRankSum=-8.100e-02;SOR=1.075	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1184,0,1467
-20	10185892	.	A	T	1257.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.21;ClippingRankSum=0.942;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQRankSum=-9.420e-01;QD=15.15;ReadPosRankSum=-7.400e-01;SOR=0.664	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1265,0,1615
-20	10186146	.	T	C	1131.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.323e+00;ClippingRankSum=0.044;DP=79;ExcessHet=3.0103;FS=9.335;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=1.65;QD=14.32;ReadPosRankSum=0.172;SOR=1.018	GT:AD:DP:GQ:PL	0/1:41,38:79:99:1139,0,1450
+20	10185892	.	A	T	1257.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.21;ClippingRankSum=0.942;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQRankSum=-9.420e-01;QD=15.15;ReadPosRankSum=-7.400e-01;SOR=0.664	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1265,0,1615
+20	10186146	.	T	C	1131.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.323e+00;ClippingRankSum=0.044;DP=79;ExcessHet=3.0103;FS=9.335;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=1.65;QD=14.32;ReadPosRankSum=0.172;SOR=1.018	GT:AD:DP:GQ:PL	0/1:41,38:79:99:1139,0,1450
 20	10186371	.	CT	C	1047.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.25;ClippingRankSum=-8.260e-01;DP=77;ExcessHet=3.0103;FS=9.959;MLEAC=1;MLEAF=0.500;MQ=60.28;MQRankSum=-6.090e-01;QD=14.16;ReadPosRankSum=0.196;SOR=1.024	GT:AD:DP:GQ:PL	0/1:33,41:74:99:1055,0,803
-20	10187086	.	T	C	1213.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.897e+00;ClippingRankSum=-7.470e-01;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.65;MQRankSum=-4.287e+00;QD=12.26;ReadPosRankSum=-3.220e-01;SOR=0.706	GT:AD:DP:GQ:PL	0/1:57,42:99:99:1221,0,1998
+20	10187086	.	T	C	1213.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.897e+00;ClippingRankSum=-7.470e-01;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.65;MQRankSum=-4.287e+00;QD=12.26;ReadPosRankSum=-3.220e-01;SOR=0.706	GT:AD:DP:GQ:PL	0/1:57,42:99:99:1221,0,1998
 20	10187114	.	CAACCTCATTCTTTTGCAAATG	C	1345.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;ClippingRankSum=-2.555e+00;DP=97;ExcessHet=3.0103;FS=2.845;MLEAC=1;MLEAF=0.500;MQ=52.49;MQRankSum=-6.115e+00;QD=15.47;ReadPosRankSum=-4.880e-01;SOR=0.652	GT:AD:DP:GQ:PL	0/1:51,36:87:99:1353,0,3591
 20	10187643	.	CA	C	960.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.27;ClippingRankSum=0.518;DP=75;ExcessHet=3.0103;FS=0.918;MLEAC=1;MLEAF=0.500;MQ=59.98;MQRankSum=-1.129e+00;QD=13.72;ReadPosRankSum=0.560;SOR=0.902	GT:AD:DP:GQ:PL	0/1:33,37:70:99:968,0,837
-20	10187868	.	T	C	1276.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.793e+00;ClippingRankSum=0.164;DP=89;ExcessHet=3.0103;FS=2.848;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=-1.470e-01;QD=14.51;ReadPosRankSum=-6.300e-02;SOR=0.616	GT:AD:DP:GQ:PL	0/1:50,38:88:99:1284,0,1792
-20	10187978	.	C	T	1298.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.37;ClippingRankSum=1.43;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.700e-01;QD=16.65;ReadPosRankSum=1.95;SOR=0.703	GT:AD:DP:GQ:PL	0/1:41,37:78:99:1306,0,1236
-20	10188245	.	G	A	1315.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.86;ClippingRankSum=1.21;DP=98;ExcessHet=3.0103;FS=2.743;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=0.143;QD=13.56;ReadPosRankSum=-9.200e-02;SOR=1.058	GT:AD:DP:GQ:PL	0/1:57,40:97:99:1323,0,1989
-20	10188428	.	C	T	3401.03	.	AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.44;QD=28.44;SOR=1.554	GT:AD:DP:GQ:PL	1/1:0,83:83:99:3415,250,0
-20	10188440	.	A	G	1317.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.581e+00;ClippingRankSum=-7.500e-02;DP=85;ExcessHet=3.0103;FS=2.970;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.084;QD=15.50;ReadPosRankSum=1.20;SOR=1.119	GT:AD:DP:GQ:PL	0/1:44,41:85:99:1325,0,1520
-20	10188612	.	A	C	1601.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.547;ClippingRankSum=-6.230e-01;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.870;QD=19.77;ReadPosRankSum=0.689;SOR=0.632	GT:AD:DP:GQ:PL	0/1:36,45:81:99:1609,0,1226
+20	10187868	.	T	C	1276.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.793e+00;ClippingRankSum=0.164;DP=89;ExcessHet=3.0103;FS=2.848;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=-1.470e-01;QD=14.51;ReadPosRankSum=-6.300e-02;SOR=0.616	GT:AD:DP:GQ:PL	0/1:50,38:88:99:1284,0,1792
+20	10187978	.	C	T	1298.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.37;ClippingRankSum=1.43;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.700e-01;QD=16.65;ReadPosRankSum=1.95;SOR=0.703	GT:AD:DP:GQ:PL	0/1:41,37:78:99:1306,0,1236
+20	10188245	.	G	A	1315.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.86;ClippingRankSum=1.21;DP=98;ExcessHet=3.0103;FS=2.743;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=0.143;QD=13.56;ReadPosRankSum=-9.200e-02;SOR=1.058	GT:AD:DP:GQ:PL	0/1:57,40:97:99:1323,0,1989
+20	10188428	.	C	T	3401.06	.	AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.44;QD=28.44;SOR=1.554	GT:AD:DP:GQ:PL	1/1:0,83:83:99:3415,250,0
+20	10188440	.	A	G	1317.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.581e+00;ClippingRankSum=-7.500e-02;DP=85;ExcessHet=3.0103;FS=2.970;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=0.084;QD=15.50;ReadPosRankSum=1.20;SOR=1.119	GT:AD:DP:GQ:PL	0/1:44,41:85:99:1325,0,1520
+20	10188612	.	A	C	1601.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.547;ClippingRankSum=-6.230e-01;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.870;QD=19.77;ReadPosRankSum=0.689;SOR=0.632	GT:AD:DP:GQ:PL	0/1:36,45:81:99:1609,0,1226
 20	10189496	.	CT	C	746.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.650e-01;ClippingRankSum=1.22;DP=94;ExcessHet=3.0103;FS=0.874;MLEAC=1;MLEAF=0.500;MQ=60.12;MQRankSum=1.87;QD=10.23;ReadPosRankSum=-1.090e-01;SOR=0.511	GT:AD:DP:GQ:PL	0/1:38,35:76:99:754,0,926
-20	10190093	.	A	C	1292.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.810e+00;ClippingRankSum=1.34;DP=76;ExcessHet=3.0103;FS=10.336;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.346;QD=17.01;ReadPosRankSum=1.42;SOR=0.172	GT:AD:DP:GQ:PL	0/1:33,43:76:99:1300,0,1114
-20	10191904	.	C	CT	1096.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.347e+00;ClippingRankSum=0.942;DP=81;ExcessHet=3.0103;FS=19.462;MLEAC=1;MLEAF=0.500;MQ=60.80;MQRankSum=1.04;QD=14.62;ReadPosRankSum=-4.310e-01;SOR=0.556	GT:AD:DP:GQ:PL	0/1:34,41:75:99:1104,0,880
-20	10193271	.	A	G	1228.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167e+00;ClippingRankSum=0.535;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.959;QD=13.07;ReadPosRankSum=-2.700e-02;SOR=0.627	GT:AD:DP:GQ:PL	0/1:56,38:94:99:1236,0,1990
-20	10193294	.	A	G	1327.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.713e+00;ClippingRankSum=2.01;DP=93;ExcessHet=3.0103;FS=2.750;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-3.110e-01;QD=14.43;ReadPosRankSum=-5.080e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:52,40:92:99:1335,0,1861
-20	10194246	.	T	C	999.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.770e-01;ClippingRankSum=0.086;DP=75;ExcessHet=3.0103;FS=10.074;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.600;QD=13.88;ReadPosRankSum=1.18;SOR=0.440	GT:AD:DP:GQ:PL	0/1:42,30:72:99:1007,0,1472
+20	10190093	.	A	C	1292.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.810e+00;ClippingRankSum=1.34;DP=76;ExcessHet=3.0103;FS=10.336;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.346;QD=17.01;ReadPosRankSum=1.42;SOR=0.172	GT:AD:DP:GQ:PL	0/1:33,43:76:99:1300,0,1114
+20	10191904	.	C	CT	1096.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.347e+00;ClippingRankSum=0.942;DP=81;ExcessHet=3.0103;FS=19.462;MLEAC=1;MLEAF=0.500;MQ=60.80;MQRankSum=1.04;QD=14.62;ReadPosRankSum=-4.310e-01;SOR=0.556	GT:AD:DP:GQ:PL	0/1:34,41:75:99:1104,0,880
+20	10193271	.	A	G	1228.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167e+00;ClippingRankSum=0.535;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.959;QD=13.07;ReadPosRankSum=-2.700e-02;SOR=0.627	GT:AD:DP:GQ:PL	0/1:56,38:94:99:1236,0,1990
+20	10193294	.	A	G	1327.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.713e+00;ClippingRankSum=2.01;DP=93;ExcessHet=3.0103;FS=2.750;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-3.110e-01;QD=14.43;ReadPosRankSum=-5.080e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:52,40:92:99:1335,0,1861
+20	10194246	.	T	C	999.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.770e-01;ClippingRankSum=0.086;DP=75;ExcessHet=3.0103;FS=10.074;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=0.600;QD=13.88;ReadPosRankSum=1.18;SOR=0.440	GT:AD:DP:GQ:PL	0/1:42,30:72:99:1007,0,1472
 20	10194560	.	AC	A	1246.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;ClippingRankSum=-8.830e-01;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=-3.450e-01;QD=15.39;ReadPosRankSum=-8.930e-01;SOR=0.752	GT:AD:DP:GQ:PL	0/1:41,40:81:99:1254,0,1287
-20	10195433	.	T	G	1156.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;ClippingRankSum=-8.350e-01;DP=73;ExcessHet=3.0103;FS=1.949;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=2.28;QD=15.84;ReadPosRankSum=-6.800e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:39,34:73:99:1164,0,1367
-20	10197086	.	T	C	787.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.507e+00;ClippingRankSum=-4.730e-01;DP=67;ExcessHet=3.0103;FS=0.966;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=-6.420e-01;QD=11.76;ReadPosRankSum=0.914;SOR=0.513	GT:AD:DP:GQ:PL	0/1:42,25:67:99:795,0,1540
-20	10197283	.	C	CT	641.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=0.259;DP=87;ExcessHet=3.0103;FS=16.131;MLEAC=1;MLEAF=0.500;MQ=60.74;MQRankSum=1.39;QD=9.17;ReadPosRankSum=-2.400e-02;SOR=2.423	GT:AD:DP:GQ:PL	0/1:37,33:70:99:649,0,762
-20	10197461	.	A	T	1050.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.367e+00;ClippingRankSum=-9.290e-01;DP=78;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.04;QD=13.47;ReadPosRankSum=1.78;SOR=0.818	GT:AD:DP:GQ:PL	0/1:46,32:78:99:1058,0,1733
-20	10197959	.	A	ATGTGTG,ATGTGTGTGTGTG	453.10	.	AC=1,1;AF=0.500,0.500;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.29;QD=35.95;SOR=1.022	GT:AD:DP:GQ:PL	1/2:0,3,2:5:99:470,164,138,117,0,116
-20	10198575	.	G	T	1005.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.15;ClippingRankSum=-8.670e-01;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=0.146;QD=21.86;ReadPosRankSum=1.45;SOR=0.836	GT:AD:DP:GQ:PL	0/1:18,28:46:99:1013,0,496
-20	10198954	.	A	C	589.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-3.120e-01;DP=29;ExcessHet=3.0103;FS=2.808;MLEAC=1;MLEAF=0.500;MQ=59.20;MQRankSum=1.85;QD=21.06;ReadPosRankSum=0.360;SOR=0.235	GT:AD:DP:GQ:PL	0/1:10,18:28:99:597,0,288
-20	10205882	.	G	GA	423.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.840;ClippingRankSum=0.234;DP=82;ExcessHet=3.0103;FS=3.715;MLEAC=1;MLEAF=0.500;MQ=60.03;MQRankSum=1.03;QD=8.65;ReadPosRankSum=-1.324e+00;SOR=1.220	GT:AD:DP:GQ:PL	0/1:28,21:54:99:431,0,594
-20	10208748	.	G	A	3056.03	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.53;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3070,228,0
-20	10212212	.	T	C	2298.03	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.82;QD=36.33;SOR=1.047	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2312,172,0
-20	10213095	.	C	T	3402.03	.	AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=32.31;SOR=1.139	GT:AD:DP:GQ:PL	1/1:0,84:84:99:3416,252,0
-20	10213542	.	T	C	2820.03	.	AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.15;QD=34.29;SOR=1.195	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2834,214,0
+20	10195433	.	T	G	1156.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;ClippingRankSum=-8.350e-01;DP=73;ExcessHet=3.0103;FS=1.949;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=2.28;QD=15.84;ReadPosRankSum=-6.800e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:39,34:73:99:1164,0,1367
+20	10197086	.	T	C	787.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.507e+00;ClippingRankSum=-4.730e-01;DP=67;ExcessHet=3.0103;FS=0.966;MLEAC=1;MLEAF=0.500;MQ=59.66;MQRankSum=-6.420e-01;QD=11.76;ReadPosRankSum=0.914;SOR=0.513	GT:AD:DP:GQ:PL	0/1:42,25:67:99:795,0,1540
+20	10197283	.	C	CT	641.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=0.259;DP=87;ExcessHet=3.0103;FS=16.131;MLEAC=1;MLEAF=0.500;MQ=60.74;MQRankSum=1.39;QD=9.17;ReadPosRankSum=-2.400e-02;SOR=2.423	GT:AD:DP:GQ:PL	0/1:37,33:70:99:649,0,762
+20	10197461	.	A	T	1050.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.367e+00;ClippingRankSum=-9.290e-01;DP=78;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.04;QD=13.47;ReadPosRankSum=1.78;SOR=0.818	GT:AD:DP:GQ:PL	0/1:46,32:78:99:1058,0,1733
+20	10197959	.	A	ATGTGTG,ATGTGTGTGTGTG	453.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.29;QD=35.95;SOR=1.022	GT:AD:DP:GQ:PL	1/2:0,3,2:5:99:470,164,138,117,0,116
+20	10198575	.	G	T	1005.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.15;ClippingRankSum=-8.670e-01;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=0.146;QD=21.86;ReadPosRankSum=1.45;SOR=0.836	GT:AD:DP:GQ:PL	0/1:18,28:46:99:1013,0,496
+20	10198954	.	A	C	589.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-3.120e-01;DP=29;ExcessHet=3.0103;FS=2.808;MLEAC=1;MLEAF=0.500;MQ=59.20;MQRankSum=1.85;QD=21.06;ReadPosRankSum=0.360;SOR=0.235	GT:AD:DP:GQ:PL	0/1:10,18:28:99:597,0,288
+20	10205882	.	G	GA	423.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.840;ClippingRankSum=0.234;DP=82;ExcessHet=3.0103;FS=3.715;MLEAC=1;MLEAF=0.500;MQ=60.03;MQRankSum=1.03;QD=8.64;ReadPosRankSum=-1.324e+00;SOR=1.220	GT:AD:DP:GQ:PL	0/1:28,21:54:99:431,0,594
+20	10208748	.	G	A	3056.06	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.53;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3070,228,0
+20	10212212	.	T	C	2298.06	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.82;QD=36.33;SOR=1.047	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2312,172,0
+20	10213095	.	C	T	3402.06	.	AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=32.31;SOR=1.139	GT:AD:DP:GQ:PL	1/1:0,84:84:99:3416,252,0
+20	10213542	.	T	C	2820.06	.	AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.15;QD=34.29;SOR=1.195	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2834,214,0
 20	10214833	.	AT	A	2061.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.51;ClippingRankSum=-1.687e+00;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.57;MQRankSum=1.42;QD=26.77;ReadPosRankSum=0.292;SOR=0.245	GT:AD:DP:GQ:PL	1/1:1,76:77:99:2075,202,0
-20	10216048	.	G	A	3034.03	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.44;QD=30.05;SOR=0.955	GT:AD:DP:GQ:PL	1/1:0,75:75:99:3048,226,0
-20	10217055	.	G	A	1720.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=0.414;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.891;QD=17.92;ReadPosRankSum=-6.120e-01;SOR=0.729	GT:AD:DP:GQ:PL	0/1:46,50:96:99:1728,0,1552
-20	10217336	.	C	T	1483.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.20;QD=33.30;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1497,114,0
-20	10217607	.	C	CATAA,CATAAATAA	1212.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-6.400e-02;ClippingRankSum=-8.350e-01;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.29;MQRankSum=-7.060e-01;QD=31.74;ReadPosRankSum=0.193;SOR=0.468	GT:AD:DP:GQ:PL	1/2:1,9,17:27:99:1229,701,712,328,0,355
-20	10217773	.	G	A	430.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.21;ClippingRankSum=-1.031e+00;DP=29;ExcessHet=3.0103;FS=6.237;MLEAC=1;MLEAF=0.500;MQ=58.55;MQRankSum=-8.110e-01;QD=14.85;ReadPosRankSum=-2.127e+00;SOR=2.012	GT:AD:DP:GQ:PL	0/1:16,13:29:99:438,0,560
-20	10217900	.	A	G	2359.03	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.77;QD=28.66;SOR=0.793	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2373,183,0
-20	10218155	.	C	G	1522.03	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.97;QD=25.41;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1536,129,0
-20	10219313	.	T	C	3037.03	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.00;QD=28.50;SOR=0.747	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3051,223,0
-20	10219799	.	A	G	1152.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.360e-01;ClippingRankSum=-1.410e-01;DP=62;ExcessHet=3.0103;FS=2.143;MLEAC=1;MLEAF=0.500;MQ=58.88;MQRankSum=0.734;QD=18.59;ReadPosRankSum=-1.130e-01;SOR=0.977	GT:AD:DP:GQ:PL	0/1:29,33:62:99:1160,0,995
-20	10220496	.	G	A	1046.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.20;ClippingRankSum=-4.510e-01;DP=68;ExcessHet=3.0103;FS=8.472;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=-1.488e+00;QD=15.39;ReadPosRankSum=0.945;SOR=0.700	GT:AD:DP:GQ:PL	0/1:38,30:68:99:1054,0,1335
-20	10220656	.	G	A	3008.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.19;SOR=1.103	GT:AD:DP:GQ:PL	1/1:0,73:73:99:3022,220,0
-20	10221044	.	C	T	3659.03	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.54;QD=30.73;SOR=1.046	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3673,271,0
-20	10223886	.	A	G	3831.03	.	AC=2;AF=1.00;AN=2;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.71;QD=26.72;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3845,285,0
-20	10224750	.	G	A	1626.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.263;ClippingRankSum=-1.268e+00;DP=81;ExcessHet=3.0103;FS=5.812;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.110;QD=20.08;ReadPosRankSum=-2.440e-01;SOR=0.701	GT:AD:DP:GQ:PL	0/1:34,47:81:99:1634,0,1096
-20	10230291	.	T	C	1905.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=34.02;SOR=1.302	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1919,168,0
-20	10231174	.	C	T	1402.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.832;ClippingRankSum=0.587;DP=78;ExcessHet=3.0103;FS=3.046;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-1.822e+00;QD=18.22;ReadPosRankSum=0.117;SOR=0.682	GT:AD:DP:GQ:PL	0/1:36,41:77:99:1410,0,1230
-20	10233052	.	C	G	1509.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.67;ClippingRankSum=-2.330e-01;DP=87;ExcessHet=3.0103;FS=2.910;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-1.108e+00;QD=17.35;ReadPosRankSum=0.157;SOR=1.080	GT:AD:DP:GQ:PL	0/1:44,43:87:99:1517,0,1458
-20	10233406	.	C	CT	31.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.570e-01;ClippingRankSum=-1.050e-01;DP=66;ExcessHet=3.0103;FS=1.691;MLEAC=1;MLEAF=0.500;MQ=59.98;MQRankSum=0.819;QD=1.02;ReadPosRankSum=-3.190e-01;SOR=1.274	GT:AD:DP:GQ:PL	0/1:25,6:33:39:39,0,527
-20	10234092	.	T	A	904.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.260e-01;ClippingRankSum=-4.790e-01;DP=86;ExcessHet=3.0103;FS=9.334;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=1.16;QD=10.90;ReadPosRankSum=0.829;SOR=0.976	GT:AD:DP:GQ:PL	0/1:53,30:83:99:912,0,1861
-20	10234257	.	G	A	1114.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.85;ClippingRankSum=-9.400e-02;DP=63;ExcessHet=3.0103;FS=3.523;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-6.500e-02;QD=18.27;ReadPosRankSum=-1.950e-01;SOR=0.581	GT:AD:DP:GQ:PL	0/1:29,32:61:99:1122,0,870
-20	10236231	.	A	G	1587.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.542e+00;ClippingRankSum=-4.250e-01;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQRankSum=1.24;QD=19.13;ReadPosRankSum=1.28;SOR=0.736	GT:AD:DP:GQ:PL	0/1:38,45:83:99:1595,0,1348
+20	10216048	.	G	A	3034.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.44;QD=30.05;SOR=0.955	GT:AD:DP:GQ:PL	1/1:0,75:75:99:3048,226,0
+20	10217055	.	G	A	1720.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=0.414;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.891;QD=17.92;ReadPosRankSum=-6.120e-01;SOR=0.729	GT:AD:DP:GQ:PL	0/1:46,50:96:99:1728,0,1552
+20	10217336	.	C	T	1483.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.20;QD=33.30;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,38:38:99:1497,114,0
+20	10217607	.	C	CATAA,CATAAATAA	1212.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-6.400e-02;ClippingRankSum=-8.350e-01;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.29;MQRankSum=-7.060e-01;QD=31.74;ReadPosRankSum=0.193;SOR=0.468	GT:AD:DP:GQ:PL	1/2:1,9,17:27:99:1229,701,712,328,0,355
+20	10217773	.	G	A	430.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.21;ClippingRankSum=-1.031e+00;DP=29;ExcessHet=3.0103;FS=6.237;MLEAC=1;MLEAF=0.500;MQ=58.55;MQRankSum=-8.110e-01;QD=14.85;ReadPosRankSum=-2.127e+00;SOR=2.012	GT:AD:DP:GQ:PL	0/1:16,13:29:99:438,0,560
+20	10217900	.	A	G	2359.06	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.77;QD=28.66;SOR=0.793	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2373,183,0
+20	10218155	.	C	G	1522.06	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.97;QD=25.41;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1536,129,0
+20	10219313	.	T	C	3037.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.00;QD=28.50;SOR=0.747	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3051,223,0
+20	10219799	.	A	G	1152.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.360e-01;ClippingRankSum=-1.410e-01;DP=62;ExcessHet=3.0103;FS=2.143;MLEAC=1;MLEAF=0.500;MQ=58.88;MQRankSum=0.734;QD=18.59;ReadPosRankSum=-1.130e-01;SOR=0.977	GT:AD:DP:GQ:PL	0/1:29,33:62:99:1160,0,995
+20	10220496	.	G	A	1046.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.20;ClippingRankSum=-4.510e-01;DP=68;ExcessHet=3.0103;FS=8.472;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=-1.488e+00;QD=15.39;ReadPosRankSum=0.945;SOR=0.700	GT:AD:DP:GQ:PL	0/1:38,30:68:99:1054,0,1335
+20	10220656	.	G	A	3008.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.19;SOR=1.103	GT:AD:DP:GQ:PL	1/1:0,73:73:99:3022,220,0
+20	10221044	.	C	T	3659.06	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.54;QD=30.73;SOR=1.046	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3673,271,0
+20	10223886	.	A	G	3831.06	.	AC=2;AF=1.00;AN=2;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.71;QD=26.72;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3845,285,0
+20	10224750	.	G	A	1626.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.263;ClippingRankSum=-1.268e+00;DP=81;ExcessHet=3.0103;FS=5.812;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.110;QD=20.08;ReadPosRankSum=-2.440e-01;SOR=0.701	GT:AD:DP:GQ:PL	0/1:34,47:81:99:1634,0,1096
+20	10230291	.	T	C	1905.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=34.02;SOR=1.302	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1919,168,0
+20	10231174	.	C	T	1402.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.832;ClippingRankSum=0.587;DP=78;ExcessHet=3.0103;FS=3.046;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-1.822e+00;QD=18.22;ReadPosRankSum=0.117;SOR=0.682	GT:AD:DP:GQ:PL	0/1:36,41:77:99:1410,0,1230
+20	10233052	.	C	G	1509.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.67;ClippingRankSum=-2.330e-01;DP=87;ExcessHet=3.0103;FS=2.910;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-1.108e+00;QD=17.35;ReadPosRankSum=0.157;SOR=1.080	GT:AD:DP:GQ:PL	0/1:44,43:87:99:1517,0,1458
+20	10233406	.	C	CT	31.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.570e-01;ClippingRankSum=-1.050e-01;DP=66;ExcessHet=3.0103;FS=1.691;MLEAC=1;MLEAF=0.500;MQ=59.98;MQRankSum=0.819;QD=1.02;ReadPosRankSum=-3.190e-01;SOR=1.274	GT:AD:DP:GQ:PL	0/1:25,6:33:39:39,0,527
+20	10234092	.	T	A	904.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.260e-01;ClippingRankSum=-4.790e-01;DP=86;ExcessHet=3.0103;FS=9.334;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=1.16;QD=10.90;ReadPosRankSum=0.829;SOR=0.976	GT:AD:DP:GQ:PL	0/1:53,30:83:99:912,0,1861
+20	10234257	.	G	A	1114.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.85;ClippingRankSum=-9.400e-02;DP=63;ExcessHet=3.0103;FS=3.523;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-6.500e-02;QD=18.27;ReadPosRankSum=-1.950e-01;SOR=0.581	GT:AD:DP:GQ:PL	0/1:29,32:61:99:1122,0,870
+20	10236231	.	A	G	1587.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.542e+00;ClippingRankSum=-4.250e-01;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQRankSum=1.24;QD=19.13;ReadPosRankSum=1.28;SOR=0.736	GT:AD:DP:GQ:PL	0/1:38,45:83:99:1595,0,1348
 20	10236580	.	AC	A	1622.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.340e-01;ClippingRankSum=-2.340e-01;DP=88;ExcessHet=3.0103;FS=2.870;MLEAC=1;MLEAF=0.500;MQ=59.86;MQRankSum=0.736;QD=18.44;ReadPosRankSum=0.030;SOR=1.050	GT:AD:DP:GQ:PL	0/1:41,47:88:99:1630,0,1391
-20	10237223	.	T	A	3947.03	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.61;QD=24.84;SOR=1.109	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3961,286,0
-20	10237816	.	A	G	2304.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=34.91;SOR=1.574	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2318,198,0
-20	10238336	.	T	G	2357.03	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.14;QD=25.31;SOR=0.756	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2371,191,0
-20	10238530	.	CA	C	106.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=1.36;DP=59;ExcessHet=3.0103;FS=13.088;MLEAC=1;MLEAF=0.500;MQ=50.68;MQRankSum=1.18;QD=8.20;ReadPosRankSum=-3.110e-01;SOR=2.430	GT:AD:DP:GQ:PL	0/1:7,6:18:79:114,0,79
+20	10237223	.	T	A	3947.06	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.61;QD=24.84;SOR=1.109	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3961,286,0
+20	10237816	.	A	G	2304.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=34.91;SOR=1.574	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2318,198,0
+20	10238336	.	T	G	2357.06	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.14;QD=25.31;SOR=0.756	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2371,191,0
+20	10238530	.	CA	C	106.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=1.36;DP=59;ExcessHet=3.0103;FS=13.088;MLEAC=1;MLEAF=0.500;MQ=50.68;MQRankSum=1.18;QD=8.20;ReadPosRankSum=-3.110e-01;SOR=2.430	GT:AD:DP:GQ:PL	0/1:7,6:18:79:114,0,79
 20	10240209	.	CAG	C	1438.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;ClippingRankSum=0.845;DP=83;ExcessHet=3.0103;FS=1.922;MLEAC=1;MLEAF=0.500;MQ=60.08;MQRankSum=1.50;QD=18.44;ReadPosRankSum=1.58;SOR=0.448	GT:AD:DP:GQ:PL	0/1:40,38:78:99:1446,0,1568
-20	10240238	.	G	A	1679.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.95;ClippingRankSum=0.342;DP=91;ExcessHet=3.0103;FS=1.801;MLEAC=1;MLEAF=0.500;MQ=59.60;MQRankSum=0.639;QD=18.87;ReadPosRankSum=-7.960e-01;SOR=0.922	GT:AD:DP:GQ:PL	0/1:40,49:89:99:1687,0,1070
-20	10240271	.	C	T	1810.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=-1.458e+00;DP=92;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=59.15;MQRankSum=1.32;QD=20.12;ReadPosRankSum=0.142;SOR=0.873	GT:AD:DP:GQ:PL	0/1:40,50:90:99:1818,0,1337
-20	10241286	.	G	C	1073.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.065e+00;ClippingRankSum=0.621;DP=60;ExcessHet=3.0103;FS=0.960;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=-1.302e+00;QD=17.89;ReadPosRankSum=-2.070e-01;SOR=0.569	GT:AD:DP:GQ:PL	0/1:29,31:60:99:1081,0,1017
-20	10241336	.	TACACACACAC	T,TACAC	1878.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-2.046e+00;ClippingRankSum=-1.671e+00;DP=74;ExcessHet=3.0103;FS=8.208;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.05;MQRankSum=-2.733e+00;QD=31.63;ReadPosRankSum=-1.421e+00;SOR=0.075	GT:AD:DP:GQ:PL	1/2:4,29,19:57:99:1895,723,799,1102,0,1168
-20	10241394	.	C	G	3305.03	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.74;QD=32.38;SOR=0.901	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3319,277,0
-20	10241483	.	G	C	3390.03	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.32;SOR=0.815	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3404,256,0
-20	10241811	.	C	T	1460.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.64;ClippingRankSum=-1.577e+00;DP=87;ExcessHet=3.0103;FS=0.794;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=-1.076e+00;QD=16.98;ReadPosRankSum=-8.200e-02;SOR=0.788	GT:AD:DP:GQ:PL	0/1:44,42:86:99:1468,0,1510
-20	10242011	.	A	C	1127.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.138;ClippingRankSum=-5.340e-01;DP=69;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-4.980e-01;QD=16.34;ReadPosRankSum=-3.780e-01;SOR=0.604	GT:AD:DP:GQ:PL	0/1:35,34:69:99:1135,0,1180
-20	10242394	.	C	G	1050.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.88;ClippingRankSum=-6.250e-01;DP=87;ExcessHet=3.0103;FS=23.835;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=0.573;QD=12.08;ReadPosRankSum=1.53;SOR=1.128	GT:AD:DP:GQ:PL	0/1:54,33:87:99:1058,0,1873
-20	10243186	.	G	A	1183.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.42;ClippingRankSum=-1.194e+00;DP=69;ExcessHet=3.0103;FS=2.002;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-1.146e+00;QD=17.15;ReadPosRankSum=0.042;SOR=1.001	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1191,0,1172
+20	10240238	.	G	A	1679.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.95;ClippingRankSum=0.342;DP=91;ExcessHet=3.0103;FS=1.801;MLEAC=1;MLEAF=0.500;MQ=59.60;MQRankSum=0.639;QD=18.87;ReadPosRankSum=-7.960e-01;SOR=0.922	GT:AD:DP:GQ:PL	0/1:40,49:89:99:1687,0,1070
+20	10240271	.	C	T	1810.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=-1.458e+00;DP=92;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=59.15;MQRankSum=1.32;QD=20.12;ReadPosRankSum=0.142;SOR=0.873	GT:AD:DP:GQ:PL	0/1:40,50:90:99:1818,0,1337
+20	10241286	.	G	C	1073.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.065e+00;ClippingRankSum=0.621;DP=60;ExcessHet=3.0103;FS=0.960;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=-1.302e+00;QD=17.89;ReadPosRankSum=-2.070e-01;SOR=0.569	GT:AD:DP:GQ:PL	0/1:29,31:60:99:1081,0,1017
+20	10241336	.	TACACACACAC	T,TACAC	1878.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-2.046e+00;ClippingRankSum=-1.671e+00;DP=74;ExcessHet=3.0103;FS=8.208;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.05;MQRankSum=-2.733e+00;QD=31.63;ReadPosRankSum=-1.421e+00;SOR=0.075	GT:AD:DP:GQ:PL	1/2:4,29,19:57:99:1895,723,799,1102,0,1168
+20	10241394	.	C	G	3305.06	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.74;QD=32.38;SOR=0.901	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3319,277,0
+20	10241483	.	G	C	3390.06	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.32;SOR=0.815	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3404,256,0
+20	10241811	.	C	T	1460.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.64;ClippingRankSum=-1.577e+00;DP=87;ExcessHet=3.0103;FS=0.794;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=-1.076e+00;QD=16.98;ReadPosRankSum=-8.200e-02;SOR=0.788	GT:AD:DP:GQ:PL	0/1:44,42:86:99:1468,0,1510
+20	10242011	.	A	C	1127.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.138;ClippingRankSum=-5.340e-01;DP=69;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-4.980e-01;QD=16.34;ReadPosRankSum=-3.780e-01;SOR=0.604	GT:AD:DP:GQ:PL	0/1:35,34:69:99:1135,0,1180
+20	10242394	.	C	G	1050.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.88;ClippingRankSum=-6.250e-01;DP=87;ExcessHet=3.0103;FS=23.835;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=0.573;QD=12.08;ReadPosRankSum=1.53;SOR=1.128	GT:AD:DP:GQ:PL	0/1:54,33:87:99:1058,0,1873
+20	10243186	.	G	A	1183.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.42;ClippingRankSum=-1.194e+00;DP=69;ExcessHet=3.0103;FS=2.002;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-1.146e+00;QD=17.15;ReadPosRankSum=0.042;SOR=1.001	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1191,0,1172
 20	10243233	.	TA	T	618.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.77;ClippingRankSum=-1.290e+00;DP=75;ExcessHet=3.0103;FS=3.562;MLEAC=1;MLEAF=0.500;MQ=60.29;MQRankSum=0.657;QD=9.10;ReadPosRankSum=0.930;SOR=0.357	GT:AD:DP:GQ:PL	0/1:39,29:68:99:626,0,910
-20	10244172	.	T	C	812.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.326e+00;ClippingRankSum=-6.590e-01;DP=73;ExcessHet=3.0103;FS=0.912;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-5.400e-01;QD=11.61;ReadPosRankSum=0.445;SOR=0.861	GT:AD:DP:GQ:PL	0/1:40,30:70:99:820,0,1404
-20	10244626	.	T	C	1103.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.278e+00;ClippingRankSum=0.917;DP=62;ExcessHet=3.0103;FS=17.275;MLEAC=1;MLEAF=0.500;MQ=59.33;MQRankSum=1.40;QD=18.09;ReadPosRankSum=2.54;SOR=0.500	GT:AD:DP:GQ:PL	0/1:25,36:61:99:1111,0,804
-20	10245139	.	C	T	1533.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.030;ClippingRankSum=-4.000e-02;DP=78;ExcessHet=3.0103;FS=0.857;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-2.552e+00;QD=19.66;ReadPosRankSum=0.301;SOR=0.564	GT:AD:DP:GQ:PL	0/1:35,43:78:99:1541,0,1211
-20	10246091	.	A	G	2238.03	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=25.62;SOR=0.725	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2252,184,0
-20	10246568	.	T	A	1510.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.510e-01;ClippingRankSum=-2.510e-01;DP=78;ExcessHet=3.0103;FS=1.889;MLEAC=1;MLEAF=0.500;MQ=59.88;MQRankSum=0.128;QD=19.62;ReadPosRankSum=1.24;SOR=0.550	GT:AD:DP:GQ:PL	0/1:34,43:77:99:1518,0,1121
-20	10246713	.	A	G	1238.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.044e+00;ClippingRankSum=0.950;DP=82;ExcessHet=3.0103;FS=0.838;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.50;QD=15.10;ReadPosRankSum=1.20;SOR=0.544	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1246,0,1648
-20	10246733	.	T	C	1581.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.882e+00;ClippingRankSum=-3.580e-01;DP=77;ExcessHet=3.0103;FS=7.920;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.151;QD=20.54;ReadPosRankSum=-1.400e-01;SOR=1.245	GT:AD:DP:GQ:PL	0/1:31,46:77:99:1589,0,1078
-20	10246815	.	A	G	1362.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.834e+00;ClippingRankSum=0.215;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=-2.462e+00;QD=19.19;ReadPosRankSum=-2.150e-01;SOR=0.618	GT:AD:DP:GQ:PL	0/1:30,41:71:99:1370,0,1019
-20	10246864	.	T	C	2517.03	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.42;QD=32.70;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2531,190,0
-20	10248123	.	A	T	1404.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.980e+00;ClippingRankSum=0.594;DP=76;ExcessHet=3.0103;FS=11.492;MLEAC=1;MLEAF=0.500;MQ=61.03;MQRankSum=2.62;QD=18.48;ReadPosRankSum=-6.250e-01;SOR=0.833	GT:AD:DP:GQ:PL	0/1:35,41:76:99:1412,0,1231
+20	10244172	.	T	C	812.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.326e+00;ClippingRankSum=-6.590e-01;DP=73;ExcessHet=3.0103;FS=0.912;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-5.400e-01;QD=11.61;ReadPosRankSum=0.445;SOR=0.861	GT:AD:DP:GQ:PL	0/1:40,30:70:99:820,0,1404
+20	10244626	.	T	C	1103.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.278e+00;ClippingRankSum=0.917;DP=62;ExcessHet=3.0103;FS=17.275;MLEAC=1;MLEAF=0.500;MQ=59.33;MQRankSum=1.40;QD=18.09;ReadPosRankSum=2.54;SOR=0.500	GT:AD:DP:GQ:PL	0/1:25,36:61:99:1111,0,804
+20	10245139	.	C	T	1533.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.030;ClippingRankSum=-4.000e-02;DP=78;ExcessHet=3.0103;FS=0.857;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-2.552e+00;QD=19.66;ReadPosRankSum=0.301;SOR=0.564	GT:AD:DP:GQ:PL	0/1:35,43:78:99:1541,0,1211
+20	10246091	.	A	G	2238.06	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=25.62;SOR=0.725	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2252,184,0
+20	10246568	.	T	A	1510.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.510e-01;ClippingRankSum=-2.510e-01;DP=78;ExcessHet=3.0103;FS=1.889;MLEAC=1;MLEAF=0.500;MQ=59.88;MQRankSum=0.128;QD=19.62;ReadPosRankSum=1.24;SOR=0.550	GT:AD:DP:GQ:PL	0/1:34,43:77:99:1518,0,1121
+20	10246713	.	A	G	1238.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.044e+00;ClippingRankSum=0.950;DP=82;ExcessHet=3.0103;FS=0.838;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.50;QD=15.11;ReadPosRankSum=1.20;SOR=0.544	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1246,0,1648
+20	10246733	.	T	C	1581.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.882e+00;ClippingRankSum=-3.580e-01;DP=77;ExcessHet=3.0103;FS=7.920;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.151;QD=20.54;ReadPosRankSum=-1.400e-01;SOR=1.245	GT:AD:DP:GQ:PL	0/1:31,46:77:99:1589,0,1078
+20	10246815	.	A	G	1362.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.834e+00;ClippingRankSum=0.215;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=-2.462e+00;QD=19.19;ReadPosRankSum=-2.150e-01;SOR=0.618	GT:AD:DP:GQ:PL	0/1:30,41:71:99:1370,0,1019
+20	10246864	.	T	C	2517.06	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.42;QD=32.70;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,63:63:99:2531,190,0
+20	10248123	.	A	T	1404.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.980e+00;ClippingRankSum=0.594;DP=76;ExcessHet=3.0103;FS=11.492;MLEAC=1;MLEAF=0.500;MQ=61.03;MQRankSum=2.62;QD=18.48;ReadPosRankSum=-6.250e-01;SOR=0.833	GT:AD:DP:GQ:PL	0/1:35,41:76:99:1412,0,1231
 20	10248188	.	TTTTG	T	1779.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;ClippingRankSum=-7.140e-01;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=2.42;QD=19.77;ReadPosRankSum=0.394;SOR=0.690	GT:AD:DP:GQ:PL	0/1:44,46:90:99:1787,0,1775
-20	10248480	.	A	G	1377.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.489e+00;ClippingRankSum=-1.542e+00;DP=95;ExcessHet=3.0103;FS=3.921;MLEAC=1;MLEAF=0.500;MQ=58.87;MQRankSum=0.290;QD=14.97;ReadPosRankSum=-1.377e+00;SOR=1.125	GT:AD:DP:GQ:PL	0/1:49,43:92:99:1385,0,1693
-20	10248574	.	G	A	1034.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;ClippingRankSum=-2.150e-01;DP=64;ExcessHet=3.0103;FS=2.069;MLEAC=1;MLEAF=0.500;MQ=58.91;MQRankSum=-9.540e-01;QD=16.17;ReadPosRankSum=-8.600e-01;SOR=0.985	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1042,0,1125
-20	10249534	.	A	G	691.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.922e+00;ClippingRankSum=-4.790e-01;DP=60;ExcessHet=3.0103;FS=3.586;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=-7.530e-01;QD=11.72;ReadPosRankSum=-6.800e-02;SOR=0.760	GT:AD:DP:GQ:PL	0/1:32,27:59:99:699,0,1126
-20	10249652	.	C	CA	1187.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.650e-01;ClippingRankSum=0.709;DP=89;ExcessHet=3.0103;FS=1.734;MLEAC=1;MLEAF=0.500;MQ=60.16;MQRankSum=0.095;QD=13.81;ReadPosRankSum=-8.560e-01;SOR=0.902	GT:AD:DP:GQ:PL	0/1:45,41:86:99:1195,0,1343
+20	10248480	.	A	G	1377.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.489e+00;ClippingRankSum=-1.542e+00;DP=95;ExcessHet=3.0103;FS=3.921;MLEAC=1;MLEAF=0.500;MQ=58.87;MQRankSum=0.290;QD=14.97;ReadPosRankSum=-1.377e+00;SOR=1.125	GT:AD:DP:GQ:PL	0/1:49,43:92:99:1385,0,1693
+20	10248574	.	G	A	1034.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;ClippingRankSum=-2.150e-01;DP=64;ExcessHet=3.0103;FS=2.069;MLEAC=1;MLEAF=0.500;MQ=58.91;MQRankSum=-9.540e-01;QD=16.17;ReadPosRankSum=-8.600e-01;SOR=0.985	GT:AD:DP:GQ:PL	0/1:33,31:64:99:1042,0,1125
+20	10249534	.	A	G	691.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.922e+00;ClippingRankSum=-4.790e-01;DP=60;ExcessHet=3.0103;FS=3.586;MLEAC=1;MLEAF=0.500;MQ=59.30;MQRankSum=-7.530e-01;QD=11.72;ReadPosRankSum=-6.800e-02;SOR=0.760	GT:AD:DP:GQ:PL	0/1:32,27:59:99:699,0,1126
+20	10249652	.	C	CA	1187.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.650e-01;ClippingRankSum=0.709;DP=89;ExcessHet=3.0103;FS=1.734;MLEAC=1;MLEAF=0.500;MQ=60.16;MQRankSum=0.095;QD=13.81;ReadPosRankSum=-8.560e-01;SOR=0.902	GT:AD:DP:GQ:PL	0/1:45,41:86:99:1195,0,1343
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf
index 21cc2f84bd2..14f6fbd0a08 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf
@@ -13,8 +13,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Thu Jun 09 17:26:25 EDT 2016",Epoch=1465507585958,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=src/test/resources/large/human_g1k_v37.20.21.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport  --genomicsdb-workspace-path /var/folders/56/l8cj86792b773xql3374k3dcmtd1k5/T/genomicsDBWorkspace3669587724853231562/workspace --variant /Users/davidben/broad/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf --intervals 21:1-11000000 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --batch-size 0 --consolidate false --validate-sample-name-map false --merge-input-intervals false --reader-threads 1 --max-num-intervals-to-import-in-parallel 1 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=Unavailable,Date="January 27, 2019 1:18:32 AM EST">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf --variant gendb:///var/folders/56/l8cj86792b773xql3374k3dcmtd1k5/T/genomicsDBWorkspace3669587724853231562/workspace --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:18:34 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -37,596 +35,594 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/louisb/Workspace/gatk-protected/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenomicsDBImport
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-21	10002403	.	G	A	40.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.67;ClippingRankSum=-6.700e-02;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.91;MQRankSum=-1.666e+00;QD=4.51;ReadPosRankSum=0.067;SOR=0.551	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,2:9:48:0|1:10002403_G_A:48,0,385
-21	10002436	.	T	G	30.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;ClippingRankSum=-7.960e-01;DP=55;ExcessHet=3.0103;FS=14.592;MLEAC=1;MLEAF=0.500;MQ=25.22;MQRankSum=2.74;QD=0.56;ReadPosRankSum=0.715;SOR=3.682	GT:AD:DP:GQ:PL	0/1:49,6:55:38:38,0,1184
-21	10002454	.	T	A	74.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015e+00;ClippingRankSum=-3.780e-01;DP=73;ExcessHet=3.0103;FS=26.186;MLEAC=1;MLEAF=0.500;MQ=24.94;MQRankSum=3.58;QD=1.02;ReadPosRankSum=-1.518e+00;SOR=4.612	GT:AD:DP:GQ:PL	0/1:64,9:73:82:82,0,1564
-21	10002529	.	A	G	172.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.720e-01;ClippingRankSum=-3.280e-01;DP=43;ExcessHet=3.0103;FS=22.523;MLEAC=1;MLEAF=0.500;MQ=25.22;MQRankSum=2.67;QD=4.01;ReadPosRankSum=2.39;SOR=4.403	GT:AD:DP:GQ:PL	0/1:35,8:43:99:180,0,843
-21	10002572	.	C	T	117.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.729;ClippingRankSum=-7.290e-01;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.59;MQRankSum=-3.610e-01;QD=13.07;ReadPosRankSum=0.00;SOR=0.527	GT:AD:DP:GQ:PL	0/1:5,4:9:99:125,0,118
-21	10002573	.	C	G	33.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;ClippingRankSum=0.762;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.59;MQRankSum=0.067;QD=3.73;ReadPosRankSum=1.67;SOR=0.132	GT:AD:DP:GQ:PL	0/1:7,2:9:41:41,0,264
-21	10002764	.	A	G	311.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.060e-01;ClippingRankSum=0.701;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.65;MQRankSum=-2.596e+00;QD=5.77;ReadPosRankSum=-1.549e+00;SOR=0.573	GT:AD:DP:GQ:PL	0/1:40,14:54:99:319,0,1316
-21	10002805	.	C	T	774.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;ClippingRankSum=-1.520e+00;DP=83;ExcessHet=3.0103;FS=1.893;MLEAC=1;MLEAF=0.500;MQ=38.61;MQRankSum=-4.252e+00;QD=9.33;ReadPosRankSum=0.173;SOR=0.463	GT:AD:DP:GQ:PL	0/1:51,32:83:99:782,0,1627
-21	10002806	.	C	T	135.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.619e+00;ClippingRankSum=0.720;DP=83;ExcessHet=3.0103;FS=5.799;MLEAC=1;MLEAF=0.500;MQ=38.61;MQRankSum=-2.183e+00;QD=1.72;ReadPosRankSum=1.58;SOR=1.483	GT:AD:DP:GQ:PL	0/1:67,12:82:99:143,0,2772
-21	10002846	.	A	G	140.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.194e+00;ClippingRankSum=2.10;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.28;MQRankSum=-9.770e-01;QD=3.35;ReadPosRankSum=-2.995e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:34,8:42:99:148,0,1099
-21	10003057	.	T	TTA	258.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=0.381;DP=73;ExcessHet=3.0103;FS=2.818;MLEAC=1;MLEAF=0.500;MQ=36.46;MQRankSum=-8.720e-01;QD=4.11;ReadPosRankSum=1.50;SOR=0.660	GT:AD:DP:GQ:PL	0/1:56,7:67:99:266,0,2300
-21	10003060	.	T	C	369.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.830e-01;ClippingRankSum=-9.130e-01;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.10;MQRankSum=-5.600e-01;QD=5.36;ReadPosRankSum=0.867;SOR=0.559	GT:AD:DP:GQ:PL	0/1:56,13:69:99:377,0,2284
-21	10003099	.	C	A	522.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;ClippingRankSum=0.143;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.55;MQRankSum=-4.400e-01;QD=6.97;ReadPosRankSum=-4.900e-01;SOR=0.576	GT:AD:DP:GQ:PGT:PID:PL	0/1:57,18:75:99:0|1:10003099_C_A:530,0,2160
-21	10003121	.	G	A	517.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.984e+00;ClippingRankSum=0.680;DP=57;ExcessHet=3.0103;FS=1.468;MLEAC=1;MLEAF=0.500;MQ=34.91;MQRankSum=0.843;QD=9.08;ReadPosRankSum=-1.296e+00;SOR=0.323	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,15:57:99:0|1:10003099_C_A:525,0,1729
-21	10003136	.	T	C	38.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.390;ClippingRankSum=-7.230e-01;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.51;MQRankSum=-2.560e+00;QD=1.29;ReadPosRankSum=0.00;SOR=0.052	GT:AD:DP:GQ:PL	0/1:25,5:30:46:46,0,868
+21	10002403	.	G	A	40.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.67;ClippingRankSum=-6.700e-02;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.91;MQRankSum=-1.666e+00;QD=4.52;ReadPosRankSum=0.067;SOR=0.551	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,2:9:48:0|1:10002403_G_A:48,0,385
+21	10002436	.	T	G	30.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;ClippingRankSum=-7.960e-01;DP=55;ExcessHet=3.0103;FS=14.592;MLEAC=1;MLEAF=0.500;MQ=25.22;MQRankSum=2.74;QD=0.56;ReadPosRankSum=0.715;SOR=3.682	GT:AD:DP:GQ:PL	0/1:49,6:55:38:38,0,1184
+21	10002454	.	T	A	74.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015e+00;ClippingRankSum=-3.780e-01;DP=73;ExcessHet=3.0103;FS=26.186;MLEAC=1;MLEAF=0.500;MQ=24.94;MQRankSum=3.58;QD=1.02;ReadPosRankSum=-1.518e+00;SOR=4.612	GT:AD:DP:GQ:PL	0/1:64,9:73:82:82,0,1564
+21	10002529	.	A	G	172.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.720e-01;ClippingRankSum=-3.280e-01;DP=43;ExcessHet=3.0103;FS=22.523;MLEAC=1;MLEAF=0.500;MQ=25.22;MQRankSum=2.67;QD=4.01;ReadPosRankSum=2.39;SOR=4.403	GT:AD:DP:GQ:PL	0/1:35,8:43:99:180,0,843
+21	10002572	.	C	T	117.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.729;ClippingRankSum=-7.290e-01;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.59;MQRankSum=-3.610e-01;QD=13.07;ReadPosRankSum=0.00;SOR=0.527	GT:AD:DP:GQ:PL	0/1:5,4:9:99:125,0,118
+21	10002573	.	C	G	33.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;ClippingRankSum=0.762;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.59;MQRankSum=0.067;QD=3.74;ReadPosRankSum=1.67;SOR=0.132	GT:AD:DP:GQ:PL	0/1:7,2:9:41:41,0,264
+21	10002764	.	A	G	311.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.060e-01;ClippingRankSum=0.701;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.65;MQRankSum=-2.596e+00;QD=5.77;ReadPosRankSum=-1.549e+00;SOR=0.573	GT:AD:DP:GQ:PL	0/1:40,14:54:99:319,0,1316
+21	10002805	.	C	T	774.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;ClippingRankSum=-1.520e+00;DP=83;ExcessHet=3.0103;FS=1.893;MLEAC=1;MLEAF=0.500;MQ=38.61;MQRankSum=-4.252e+00;QD=9.33;ReadPosRankSum=0.173;SOR=0.463	GT:AD:DP:GQ:PL	0/1:51,32:83:99:782,0,1627
+21	10002806	.	C	T	135.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.619e+00;ClippingRankSum=0.720;DP=83;ExcessHet=3.0103;FS=5.799;MLEAC=1;MLEAF=0.500;MQ=38.61;MQRankSum=-2.183e+00;QD=1.72;ReadPosRankSum=1.58;SOR=1.483	GT:AD:DP:GQ:PL	0/1:67,12:82:99:143,0,2772
+21	10002846	.	A	G	140.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.194e+00;ClippingRankSum=2.10;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.28;MQRankSum=-9.770e-01;QD=3.35;ReadPosRankSum=-2.995e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:34,8:42:99:148,0,1099
+21	10003057	.	T	TTA	258.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=0.381;DP=73;ExcessHet=3.0103;FS=2.818;MLEAC=1;MLEAF=0.500;MQ=36.46;MQRankSum=-8.720e-01;QD=4.10;ReadPosRankSum=1.50;SOR=0.660	GT:AD:DP:GQ:PL	0/1:56,7:67:99:266,0,2300
+21	10003060	.	T	C	369.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.830e-01;ClippingRankSum=-9.130e-01;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.10;MQRankSum=-5.600e-01;QD=5.36;ReadPosRankSum=0.867;SOR=0.559	GT:AD:DP:GQ:PL	0/1:56,13:69:99:377,0,2284
+21	10003099	.	C	A	522.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;ClippingRankSum=0.143;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.55;MQRankSum=-4.400e-01;QD=6.97;ReadPosRankSum=-4.900e-01;SOR=0.576	GT:AD:DP:GQ:PGT:PID:PL	0/1:57,18:75:99:0|1:10003099_C_A:530,0,2160
+21	10003121	.	G	A	517.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.984e+00;ClippingRankSum=0.680;DP=57;ExcessHet=3.0103;FS=1.468;MLEAC=1;MLEAF=0.500;MQ=34.91;MQRankSum=0.843;QD=9.08;ReadPosRankSum=-1.296e+00;SOR=0.323	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,15:57:99:0|1:10003099_C_A:525,0,1729
+21	10003136	.	T	C	38.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.390;ClippingRankSum=-7.230e-01;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.51;MQRankSum=-2.560e+00;QD=1.29;ReadPosRankSum=0.00;SOR=0.052	GT:AD:DP:GQ:PL	0/1:25,5:30:46:46,0,868
 21	10005032	.	CT	C	43.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;ClippingRankSum=0.935;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.14;MQRankSum=0.377;QD=3.96;ReadPosRankSum=0.935;SOR=0.495	GT:AD:DP:GQ:PL	0/1:7,4:13:51:51,0,189
-21	10005583	.	G	A	46.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.720;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=-1.380e+00;QD=7.77;ReadPosRankSum=-1.380e+00;SOR=0.307	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,2:6:54:1|0:10005578_G_T:54,0,179
-21	10005844	.	A	G	93.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.598e+00;ClippingRankSum=-6.020e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.19;MQRankSum=-8.280e-01;QD=2.46;ReadPosRankSum=-2.485e+00;SOR=0.735	GT:AD:DP:GQ:PL	0/1:31,7:38:99:101,0,847
-21	10005921	.	C	T	1037.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.78;ClippingRankSum=-6.150e-01;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.71;MQRankSum=1.84;QD=19.21;ReadPosRankSum=2.80;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,28:54:99:0|1:10005921_C_T:1045,0,844
-21	10005937	.	T	TA	1070.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.574;ClippingRankSum=-1.300e-02;DP=42;ExcessHet=3.0103;FS=1.283;MLEAC=1;MLEAF=0.500;MQ=26.43;MQRankSum=1.03;QD=25.49;ReadPosRankSum=-1.200e-01;SOR=0.648	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,28:42:99:0|1:10005921_C_T:1078,0,572
-21	10006989	.	A	G	102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.210e-01;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.87;MQRankSum=0.421;QD=12.83;ReadPosRankSum=0.421;SOR=0.693	GT:AD:DP:GQ:PL	0/1:4,4:8:99:110,0,102
-21	10007000	.	C	T	87.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;ClippingRankSum=0.077;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.45;MQRankSum=1.47;QD=6.74;ReadPosRankSum=-7.700e-02;SOR=1.508	GT:AD:DP:GQ:PL	0/1:9,4:13:95:95,0,240
-21	10007251	.	T	C	54.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.266e+00;ClippingRankSum=0.381;DP=49;ExcessHet=3.0103;FS=27.121;MLEAC=1;MLEAF=0.500;MQ=31.81;MQRankSum=-1.500e-02;QD=1.11;ReadPosRankSum=-2.211e+00;SOR=3.896	GT:AD:DP:GQ:PL	0/1:43,6:49:62:62,0,1310
-21	10007293	.	A	G	88.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.992e+00;ClippingRankSum=1.32;DP=47;ExcessHet=3.0103;FS=25.974;MLEAC=1;MLEAF=0.500;MQ=32.68;MQRankSum=-2.710e-01;QD=1.89;ReadPosRankSum=2.18;SOR=3.897	GT:AD:DP:GQ:PL	0/1:41,6:47:96:96,0,1294
-21	10008294	.	C	A	57.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=0.358;QD=11.52;ReadPosRankSum=-1.231e+00;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:38:65,0,38
-21	10008606	.	C	G	329.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.249e+00;ClippingRankSum=-7.000e-02;DP=51;ExcessHet=3.0103;FS=1.154;MLEAC=1;MLEAF=0.500;MQ=24.31;MQRankSum=-3.500e-01;QD=6.46;ReadPosRankSum=0.829;SOR=1.061	GT:AD:DP:GQ:PL	0/1:34,17:51:99:337,0,816
-21	10010445	.	A	G	42.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.906e+00;ClippingRankSum=-2.030e-01;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.96;MQRankSum=-1.014e+00;QD=1.85;ReadPosRankSum=1.10;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,4:23:50:0|1:10010422_T_C:50,0,462
-21	10010933	.	T	C	417.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.308e+00;ClippingRankSum=0.856;DP=86;ExcessHet=3.0103;FS=4.548;MLEAC=1;MLEAF=0.500;MQ=23.80;MQRankSum=0.732;QD=4.86;ReadPosRankSum=1.64;SOR=0.790	GT:AD:DP:GQ:PL	0/1:61,25:86:99:425,0,1422
-21	10010961	.	A	G	702.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.146e+00;ClippingRankSum=-1.200e-02;DP=91;ExcessHet=3.0103;FS=4.083;MLEAC=1;MLEAF=0.500;MQ=24.10;MQRankSum=1.30;QD=7.72;ReadPosRankSum=1.63;SOR=0.909	GT:AD:DP:GQ:PL	0/1:56,35:91:99:710,0,1267
-21	10012343	.	T	A	216.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=0.529;DP=35;ExcessHet=3.0103;FS=14.401;MLEAC=1;MLEAF=0.500;MQ=44.90;MQRankSum=-3.560e+00;QD=6.19;ReadPosRankSum=-7.490e-01;SOR=3.758	GT:AD:DP:GQ:PL	0/1:25,10:35:99:224,0,846
-21	10012443	.	T	C	75.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.057;ClippingRankSum=-9.620e-01;DP=17;ExcessHet=3.0103;FS=5.842;MLEAC=1;MLEAF=0.500;MQ=24.76;MQRankSum=2.77;QD=4.45;ReadPosRankSum=0.623;SOR=2.494	GT:AD:DP:GQ:PL	0/1:13,4:17:83:83,0,312
-21	10012688	.	T	A	902.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=0.959;DP=55;ExcessHet=3.0103;FS=3.944;MLEAC=1;MLEAF=0.500;MQ=34.32;MQRankSum=2.55;QD=16.41;ReadPosRankSum=4.32;SOR=0.293	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,24:55:99:0|1:10012688_T_A:910,0,1065
-21	10012704	.	T	A	954.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.291e+00;ClippingRankSum=-6.400e-01;DP=48;ExcessHet=3.0103;FS=4.167;MLEAC=1;MLEAF=0.500;MQ=33.40;MQRankSum=3.67;QD=19.89;ReadPosRankSum=3.82;SOR=0.297	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,25:48:99:0|1:10012688_T_A:962,0,813
-21	10012740	.	C	T	370.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=-8.800e-01;DP=22;ExcessHet=3.0103;FS=1.740;MLEAC=1;MLEAF=0.500;MQ=34.41;MQRankSum=1.02;QD=17.65;ReadPosRankSum=-6.690e-01;SOR=1.270	GT:AD:DP:GQ:PL	0/1:10,11:21:99:378,0,279
+21	10005583	.	G	A	46.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.720;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=-1.380e+00;QD=7.77;ReadPosRankSum=-1.380e+00;SOR=0.307	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,2:6:54:1|0:10005578_G_T:54,0,179
+21	10005844	.	A	G	93.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.598e+00;ClippingRankSum=-6.020e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.19;MQRankSum=-8.280e-01;QD=2.46;ReadPosRankSum=-2.485e+00;SOR=0.735	GT:AD:DP:GQ:PL	0/1:31,7:38:99:101,0,847
+21	10005921	.	C	T	1037.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.78;ClippingRankSum=-6.150e-01;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.71;MQRankSum=1.84;QD=19.22;ReadPosRankSum=2.80;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,28:54:99:0|1:10005921_C_T:1045,0,844
+21	10005937	.	T	TA	1070.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.574;ClippingRankSum=-1.300e-02;DP=42;ExcessHet=3.0103;FS=1.283;MLEAC=1;MLEAF=0.500;MQ=26.43;MQRankSum=1.03;QD=25.49;ReadPosRankSum=-1.200e-01;SOR=0.648	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,28:42:99:0|1:10005921_C_T:1078,0,572
+21	10006989	.	A	G	102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.210e-01;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.87;MQRankSum=0.421;QD=12.83;ReadPosRankSum=0.421;SOR=0.693	GT:AD:DP:GQ:PL	0/1:4,4:8:99:110,0,102
+21	10007000	.	C	T	87.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;ClippingRankSum=0.077;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.45;MQRankSum=1.47;QD=6.74;ReadPosRankSum=-7.700e-02;SOR=1.508	GT:AD:DP:GQ:PL	0/1:9,4:13:95:95,0,240
+21	10007251	.	T	C	54.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.266e+00;ClippingRankSum=0.381;DP=49;ExcessHet=3.0103;FS=27.121;MLEAC=1;MLEAF=0.500;MQ=31.81;MQRankSum=-1.500e-02;QD=1.12;ReadPosRankSum=-2.211e+00;SOR=3.896	GT:AD:DP:GQ:PL	0/1:43,6:49:62:62,0,1310
+21	10007293	.	A	G	88.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.992e+00;ClippingRankSum=1.32;DP=47;ExcessHet=3.0103;FS=25.974;MLEAC=1;MLEAF=0.500;MQ=32.68;MQRankSum=-2.710e-01;QD=1.89;ReadPosRankSum=2.18;SOR=3.897	GT:AD:DP:GQ:PL	0/1:41,6:47:96:96,0,1294
+21	10008294	.	C	A	57.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=0.358;QD=11.53;ReadPosRankSum=-1.231e+00;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:38:65,0,38
+21	10008606	.	C	G	329.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.249e+00;ClippingRankSum=-7.000e-02;DP=51;ExcessHet=3.0103;FS=1.154;MLEAC=1;MLEAF=0.500;MQ=24.31;MQRankSum=-3.500e-01;QD=6.46;ReadPosRankSum=0.829;SOR=1.061	GT:AD:DP:GQ:PL	0/1:34,17:51:99:337,0,816
+21	10010445	.	A	G	42.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.906e+00;ClippingRankSum=-2.030e-01;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.96;MQRankSum=-1.014e+00;QD=1.85;ReadPosRankSum=1.10;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,4:23:50:0|1:10010422_T_C:50,0,462
+21	10010933	.	T	C	417.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.308e+00;ClippingRankSum=0.856;DP=86;ExcessHet=3.0103;FS=4.548;MLEAC=1;MLEAF=0.500;MQ=23.80;MQRankSum=0.732;QD=4.86;ReadPosRankSum=1.64;SOR=0.790	GT:AD:DP:GQ:PL	0/1:61,25:86:99:425,0,1422
+21	10010961	.	A	G	702.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.146e+00;ClippingRankSum=-1.200e-02;DP=91;ExcessHet=3.0103;FS=4.083;MLEAC=1;MLEAF=0.500;MQ=24.10;MQRankSum=1.30;QD=7.72;ReadPosRankSum=1.63;SOR=0.909	GT:AD:DP:GQ:PL	0/1:56,35:91:99:710,0,1267
+21	10012343	.	T	A	216.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=0.529;DP=35;ExcessHet=3.0103;FS=14.401;MLEAC=1;MLEAF=0.500;MQ=44.90;MQRankSum=-3.560e+00;QD=6.19;ReadPosRankSum=-7.490e-01;SOR=3.758	GT:AD:DP:GQ:PL	0/1:25,10:35:99:224,0,846
+21	10012443	.	T	C	75.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.057;ClippingRankSum=-9.620e-01;DP=17;ExcessHet=3.0103;FS=5.842;MLEAC=1;MLEAF=0.500;MQ=24.76;MQRankSum=2.77;QD=4.45;ReadPosRankSum=0.623;SOR=2.494	GT:AD:DP:GQ:PL	0/1:13,4:17:83:83,0,312
+21	10012688	.	T	A	902.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=0.959;DP=55;ExcessHet=3.0103;FS=3.944;MLEAC=1;MLEAF=0.500;MQ=34.32;MQRankSum=2.55;QD=16.41;ReadPosRankSum=4.32;SOR=0.293	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,24:55:99:0|1:10012688_T_A:910,0,1065
+21	10012704	.	T	A	954.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.291e+00;ClippingRankSum=-6.400e-01;DP=48;ExcessHet=3.0103;FS=4.167;MLEAC=1;MLEAF=0.500;MQ=33.40;MQRankSum=3.67;QD=19.89;ReadPosRankSum=3.82;SOR=0.297	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,25:48:99:0|1:10012688_T_A:962,0,813
+21	10012740	.	C	T	370.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=-8.800e-01;DP=22;ExcessHet=3.0103;FS=1.740;MLEAC=1;MLEAF=0.500;MQ=34.41;MQRankSum=1.02;QD=17.65;ReadPosRankSum=-6.690e-01;SOR=1.270	GT:AD:DP:GQ:PL	0/1:10,11:21:99:378,0,279
 21	10012866	.	TG	T	286.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.44;ClippingRankSum=0.055;DP=35;ExcessHet=3.0103;FS=8.809;MLEAC=1;MLEAF=0.500;MQ=30.67;MQRankSum=-2.319e+00;QD=8.19;ReadPosRankSum=2.83;SOR=1.469	GT:AD:DP:GQ:PL	0/1:25,10:35:99:294,0,842
-21	10012891	.	A	C	158.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.015;ClippingRankSum=-1.169e+00;DP=41;ExcessHet=3.0103;FS=7.988;MLEAC=1;MLEAF=0.500;MQ=30.93;MQRankSum=-2.565e+00;QD=3.87;ReadPosRankSum=0.228;SOR=1.514	GT:AD:DP:GQ:PL	0/1:31,10:41:99:166,0,935
-21	10012928	.	T	C	166.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.242e+00;ClippingRankSum=-1.718e+00;DP=47;ExcessHet=3.0103;FS=1.610;MLEAC=1;MLEAF=0.500;MQ=30.37;MQRankSum=-1.640e-01;QD=3.54;ReadPosRankSum=-1.808e+00;SOR=0.809	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,7:47:99:0|1:10012928_T_C:174,0,1650
-21	10012929	.	T	G	166.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.362e+00;ClippingRankSum=-2.540e-01;DP=47;ExcessHet=3.0103;FS=1.610;MLEAC=1;MLEAF=0.500;MQ=30.37;MQRankSum=-1.500e-02;QD=3.54;ReadPosRankSum=-7.400e-01;SOR=0.809	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,7:47:99:0|1:10012928_T_C:174,0,1650
-21	10012994	.	T	C	288.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;ClippingRankSum=-6.410e-01;DP=39;ExcessHet=3.0103;FS=22.414;MLEAC=1;MLEAF=0.500;MQ=28.08;MQRankSum=1.59;QD=7.40;ReadPosRankSum=0.253;SOR=2.792	GT:AD:DP:GQ:PL	0/1:26,13:39:99:296,0,700
-21	10013108	.	C	T	129.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.94;ClippingRankSum=0.118;DP=31;ExcessHet=3.0103;FS=20.604;MLEAC=1;MLEAF=0.500;MQ=32.04;MQRankSum=1.63;QD=4.18;ReadPosRankSum=-6.850e-01;SOR=4.167	GT:AD:DP:GQ:PL	0/1:24,7:31:99:137,0,571
-21	10013602	.	A	C	432.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.520e-01;ClippingRankSum=0.771;DP=104;ExcessHet=3.0103;FS=4.567;MLEAC=1;MLEAF=0.500;MQ=34.17;MQRankSum=-3.514e+00;QD=4.16;ReadPosRankSum=2.16;SOR=1.276	GT:AD:DP:GQ:PL	0/1:77,27:104:99:440,0,2170
-21	10013756	.	A	C	181.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.031e+00;ClippingRankSum=0.650;DP=68;ExcessHet=3.0103;FS=4.926;MLEAC=1;MLEAF=0.500;MQ=26.44;MQRankSum=-5.230e+00;QD=2.67;ReadPosRankSum=0.699;SOR=1.132	GT:AD:DP:GQ:PGT:PID:PL	0/1:57,11:68:99:0|1:10013756_A_C:189,0,1568
-21	10014357	.	A	G	66.80	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;QD=22.27;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:80,9,0
-21	10014570	.	T	C	1282.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.490e-01;ClippingRankSum=-8.780e-01;DP=60;ExcessHet=3.0103;FS=9.366;MLEAC=1;MLEAF=0.500;MQ=25.36;MQRankSum=-5.570e-01;QD=21.74;ReadPosRankSum=1.67;SOR=0.735	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,33:59:99:0|1:10014570_T_C:1290,0,1382
-21	10014572	.	A	G	1282.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.025e+00;ClippingRankSum=-2.110e-01;DP=59;ExcessHet=3.0103;FS=9.226;MLEAC=1;MLEAF=0.500;MQ=25.40;MQRankSum=-2.244e+00;QD=22.11;ReadPosRankSum=0.993;SOR=0.649	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,32:58:99:0|1:10014570_T_C:1290,0,1382
-21	10014931	.	G	T	609.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.034;ClippingRankSum=0.491;DP=56;ExcessHet=3.0103;FS=17.092;MLEAC=1;MLEAF=0.500;MQ=36.71;MQRankSum=-2.319e+00;QD=10.89;ReadPosRankSum=1.34;SOR=3.507	GT:AD:DP:GQ:PGT:PID:PL	0/1:35,21:56:99:0|1:10014931_G_T:617,0,1078
-21	10014933	.	G	C	60.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.311e+00;ClippingRankSum=0.644;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.67;MQRankSum=-9.980e-01;QD=1.10;ReadPosRankSum=0.366;SOR=0.921	GT:AD:DP:GQ:PGT:PID:PL	0/1:48,7:55:68:0|1:10014931_G_T:68,0,2778
-21	10015178	.	G	A	478.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.600e-01;ClippingRankSum=-1.679e+00;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.05;MQRankSum=-9.000e-01;QD=8.55;ReadPosRankSum=-2.994e+00;SOR=0.748	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,19:56:99:0|1:10015178_G_A:486,0,947
-21	10017839	.	C	G	343.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;ClippingRankSum=0.508;DP=50;ExcessHet=3.0103;FS=1.523;MLEAC=1;MLEAF=0.500;MQ=33.32;MQRankSum=1.29;QD=6.87;ReadPosRankSum=2.45;SOR=1.033	GT:AD:DP:GQ:PL	0/1:36,14:50:99:351,0,1006
-21	10019012	.	G	A	385.02	.	AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.69;QD=32.09;SOR=2.670	GT:AD:DP:GQ:PL	1/1:0,12:12:36:399,36,0
-21	10020383	.	A	C	44.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.56;MQRankSum=0.736;QD=7.43;ReadPosRankSum=0.736;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,1:6:52:0|1:10020383_A_C:52,0,276
-21	10020396	.	T	C	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.192e+00;ClippingRankSum=0.071;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.16;MQRankSum=0.071;QD=6.61;ReadPosRankSum=-9.190e-01;SOR=0.188	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,4:14:99:0|1:10020383_A_C:100,0,382
-21	10020415	.	C	A	50.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.12;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.93;MQRankSum=1.41;QD=1.81;ReadPosRankSum=-6.890e-01;SOR=0.039	GT:AD:DP:GQ:PL	0/1:24,4:28:58:58,0,811
-21	10020433	.	C	A	306.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.28;ClippingRankSum=0.857;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.12;MQRankSum=-1.172e+00;QD=9.02;ReadPosRankSum=-2.012e+00;SOR=0.412	GT:AD:DP:GQ:PL	0/1:20,14:34:99:314,0,598
-21	10020472	.	G	A	89.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=-6.160e-01;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.82;MQRankSum=1.25;QD=1.76;ReadPosRankSum=0.616;SOR=0.031	GT:AD:DP:GQ:PL	0/1:44,7:51:97:97,0,1530
-21	10020481	.	G	A	848.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.62;ClippingRankSum=0.238;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.57;MQRankSum=-3.148e+00;QD=16.64;ReadPosRankSum=0.257;SOR=0.462	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,22:51:99:0|1:10020481_G_A:856,0,1038
-21	10020496	.	T	C	838.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.676e+00;ClippingRankSum=0.309;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.82;MQRankSum=-4.701e+00;QD=17.84;ReadPosRankSum=0.885;SOR=0.578	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,22:47:99:0|1:10020481_G_A:846,0,1014
-21	10020497	.	G	A	838.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.72;ClippingRankSum=-1.423e+00;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.82;MQRankSum=-5.146e+00;QD=17.84;ReadPosRankSum=1.25;SOR=0.509	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,21:47:99:0|1:10020481_G_A:846,0,1014
-21	10020715	.	T	C	498.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.435e+00;ClippingRankSum=-9.400e-02;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.30;MQRankSum=0.538;QD=4.34;ReadPosRankSum=-3.033e+00;SOR=0.624	GT:AD:DP:GQ:PL	0/1:87,28:115:99:506,0,3531
-21	10020723	.	A	T	1284.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.953e+00;ClippingRankSum=-4.850e-01;DP=124;ExcessHet=3.0103;FS=20.393;MLEAC=1;MLEAF=0.500;MQ=30.22;MQRankSum=2.73;QD=10.44;ReadPosRankSum=-4.270e+00;SOR=0.616	GT:AD:DP:GQ:PL	0/1:75,48:123:99:1292,0,1787
+21	10012891	.	A	C	158.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.015;ClippingRankSum=-1.169e+00;DP=41;ExcessHet=3.0103;FS=7.988;MLEAC=1;MLEAF=0.500;MQ=30.93;MQRankSum=-2.565e+00;QD=3.87;ReadPosRankSum=0.228;SOR=1.514	GT:AD:DP:GQ:PL	0/1:31,10:41:99:166,0,935
+21	10012928	.	T	C	166.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.242e+00;ClippingRankSum=-1.718e+00;DP=47;ExcessHet=3.0103;FS=1.610;MLEAC=1;MLEAF=0.500;MQ=30.37;MQRankSum=-1.640e-01;QD=3.55;ReadPosRankSum=-1.808e+00;SOR=0.809	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,7:47:99:0|1:10012928_T_C:174,0,1650
+21	10012929	.	T	G	166.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.362e+00;ClippingRankSum=-2.540e-01;DP=47;ExcessHet=3.0103;FS=1.610;MLEAC=1;MLEAF=0.500;MQ=30.37;MQRankSum=-1.500e-02;QD=3.55;ReadPosRankSum=-7.400e-01;SOR=0.809	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,7:47:99:0|1:10012928_T_C:174,0,1650
+21	10012994	.	T	C	288.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;ClippingRankSum=-6.410e-01;DP=39;ExcessHet=3.0103;FS=22.414;MLEAC=1;MLEAF=0.500;MQ=28.08;MQRankSum=1.59;QD=7.40;ReadPosRankSum=0.253;SOR=2.792	GT:AD:DP:GQ:PL	0/1:26,13:39:99:296,0,700
+21	10013108	.	C	T	129.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.94;ClippingRankSum=0.118;DP=31;ExcessHet=3.0103;FS=20.604;MLEAC=1;MLEAF=0.500;MQ=32.04;MQRankSum=1.63;QD=4.18;ReadPosRankSum=-6.850e-01;SOR=4.167	GT:AD:DP:GQ:PL	0/1:24,7:31:99:137,0,571
+21	10013602	.	A	C	432.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.520e-01;ClippingRankSum=0.771;DP=104;ExcessHet=3.0103;FS=4.567;MLEAC=1;MLEAF=0.500;MQ=34.17;MQRankSum=-3.514e+00;QD=4.16;ReadPosRankSum=2.16;SOR=1.276	GT:AD:DP:GQ:PL	0/1:77,27:104:99:440,0,2170
+21	10013756	.	A	C	181.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.031e+00;ClippingRankSum=0.650;DP=68;ExcessHet=3.0103;FS=4.926;MLEAC=1;MLEAF=0.500;MQ=26.44;MQRankSum=-5.230e+00;QD=2.67;ReadPosRankSum=0.699;SOR=1.132	GT:AD:DP:GQ:PGT:PID:PL	0/1:57,11:68:99:0|1:10013756_A_C:189,0,1568
+21	10014357	.	A	G	66.84	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;QD=22.28;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:80,9,0
+21	10014570	.	T	C	1282.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.490e-01;ClippingRankSum=-8.780e-01;DP=60;ExcessHet=3.0103;FS=9.366;MLEAC=1;MLEAF=0.500;MQ=25.36;MQRankSum=-5.570e-01;QD=21.74;ReadPosRankSum=1.67;SOR=0.735	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,33:59:99:0|1:10014570_T_C:1290,0,1382
+21	10014572	.	A	G	1282.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.025e+00;ClippingRankSum=-2.110e-01;DP=59;ExcessHet=3.0103;FS=9.226;MLEAC=1;MLEAF=0.500;MQ=25.40;MQRankSum=-2.244e+00;QD=22.11;ReadPosRankSum=0.993;SOR=0.649	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,32:58:99:0|1:10014570_T_C:1290,0,1382
+21	10014931	.	G	T	609.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.034;ClippingRankSum=0.491;DP=56;ExcessHet=3.0103;FS=17.092;MLEAC=1;MLEAF=0.500;MQ=36.71;MQRankSum=-2.319e+00;QD=10.89;ReadPosRankSum=1.34;SOR=3.507	GT:AD:DP:GQ:PGT:PID:PL	0/1:35,21:56:99:0|1:10014931_G_T:617,0,1078
+21	10014933	.	G	C	60.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.311e+00;ClippingRankSum=0.644;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.67;MQRankSum=-9.980e-01;QD=1.10;ReadPosRankSum=0.366;SOR=0.921	GT:AD:DP:GQ:PGT:PID:PL	0/1:48,7:55:68:0|1:10014931_G_T:68,0,2778
+21	10015178	.	G	A	478.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.600e-01;ClippingRankSum=-1.679e+00;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.05;MQRankSum=-9.000e-01;QD=8.55;ReadPosRankSum=-2.994e+00;SOR=0.748	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,19:56:99:0|1:10015178_G_A:486,0,947
+21	10017839	.	C	G	343.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;ClippingRankSum=0.508;DP=50;ExcessHet=3.0103;FS=1.523;MLEAC=1;MLEAF=0.500;MQ=33.32;MQRankSum=1.29;QD=6.87;ReadPosRankSum=2.45;SOR=1.033	GT:AD:DP:GQ:PL	0/1:36,14:50:99:351,0,1006
+21	10019012	.	G	A	385.06	.	AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.69;QD=32.09;SOR=2.670	GT:AD:DP:GQ:PL	1/1:0,12:12:36:399,36,0
+21	10020383	.	A	C	44.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.56;MQRankSum=0.736;QD=7.44;ReadPosRankSum=0.736;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,1:6:52:0|1:10020383_A_C:52,0,276
+21	10020396	.	T	C	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.192e+00;ClippingRankSum=0.071;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.16;MQRankSum=0.071;QD=6.62;ReadPosRankSum=-9.190e-01;SOR=0.188	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,4:14:99:0|1:10020383_A_C:100,0,382
+21	10020415	.	C	A	50.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.12;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.93;MQRankSum=1.41;QD=1.81;ReadPosRankSum=-6.890e-01;SOR=0.039	GT:AD:DP:GQ:PL	0/1:24,4:28:58:58,0,811
+21	10020433	.	C	A	306.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.28;ClippingRankSum=0.857;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.12;MQRankSum=-1.172e+00;QD=9.02;ReadPosRankSum=-2.012e+00;SOR=0.412	GT:AD:DP:GQ:PL	0/1:20,14:34:99:314,0,598
+21	10020472	.	G	A	89.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=-6.160e-01;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.82;MQRankSum=1.25;QD=1.76;ReadPosRankSum=0.616;SOR=0.031	GT:AD:DP:GQ:PL	0/1:44,7:51:97:97,0,1530
+21	10020481	.	G	A	848.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.62;ClippingRankSum=0.238;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.57;MQRankSum=-3.148e+00;QD=16.64;ReadPosRankSum=0.257;SOR=0.462	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,22:51:99:0|1:10020481_G_A:856,0,1038
+21	10020496	.	T	C	838.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.676e+00;ClippingRankSum=0.309;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.82;MQRankSum=-4.701e+00;QD=17.84;ReadPosRankSum=0.885;SOR=0.578	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,22:47:99:0|1:10020481_G_A:846,0,1014
+21	10020497	.	G	A	838.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.72;ClippingRankSum=-1.423e+00;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.82;MQRankSum=-5.146e+00;QD=17.84;ReadPosRankSum=1.25;SOR=0.509	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,21:47:99:0|1:10020481_G_A:846,0,1014
+21	10020715	.	T	C	498.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.435e+00;ClippingRankSum=-9.400e-02;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.30;MQRankSum=0.538;QD=4.34;ReadPosRankSum=-3.033e+00;SOR=0.624	GT:AD:DP:GQ:PL	0/1:87,28:115:99:506,0,3531
+21	10020723	.	A	T	1284.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.953e+00;ClippingRankSum=-4.850e-01;DP=124;ExcessHet=3.0103;FS=20.393;MLEAC=1;MLEAF=0.500;MQ=30.22;MQRankSum=2.73;QD=10.44;ReadPosRankSum=-4.270e+00;SOR=0.616	GT:AD:DP:GQ:PL	0/1:75,48:123:99:1292,0,1787
 21	10020752	.	AGT	A	373.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.355e+00;ClippingRankSum=0.099;DP=161;ExcessHet=3.0103;FS=5.652;MLEAC=1;MLEAF=0.500;MQ=30.59;MQRankSum=-1.950e-01;QD=5.26;ReadPosRankSum=1.07;SOR=0.296	GT:AD:DP:GQ:PL	0/1:48,23:91:99:381,0,1919
-21	10020798	.	G	A	810.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.61;ClippingRankSum=0.094;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.61;MQRankSum=-4.325e+00;QD=10.67;ReadPosRankSum=1.78;SOR=0.585	GT:AD:DP:GQ:PL	0/1:41,35:76:99:818,0,1128
-21	10020975	.	G	A	145.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=0.590;DP=54;ExcessHet=3.0103;FS=16.658;MLEAC=1;MLEAF=0.500;MQ=32.05;MQRankSum=0.189;QD=2.70;ReadPosRankSum=-6.350e-01;SOR=3.932	GT:AD:DP:GQ:PL	0/1:44,10:54:99:153,0,1192
-21	10021000	.	T	G	369.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.840e-01;ClippingRankSum=1.21;DP=56;ExcessHet=3.0103;FS=22.753;MLEAC=1;MLEAF=0.500;MQ=27.64;MQRankSum=1.23;QD=6.60;ReadPosRankSum=0.499;SOR=4.690	GT:AD:DP:GQ:PL	0/1:39,17:56:99:377,0,1010
-21	10021012	.	C	T	368.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.17;ClippingRankSum=0.017;DP=58;ExcessHet=3.0103;FS=21.916;MLEAC=1;MLEAF=0.500;MQ=27.95;MQRankSum=1.55;QD=6.36;ReadPosRankSum=2.13;SOR=4.337	GT:AD:DP:GQ:PL	0/1:41,17:58:99:376,0,1101
-21	10021100	.	C	A	128.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.900e-02;ClippingRankSum=0.147;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.56;MQRankSum=-3.430e-01;QD=4.29;ReadPosRankSum=-4.900e-01;SOR=0.395	GT:AD:DP:GQ:PL	0/1:23,7:30:99:136,0,703
-21	10021586	.	G	T	256.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.15;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=5.590;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=-3.690e-01;QD=9.16;ReadPosRankSum=2.26;SOR=1.567	GT:AD:DP:GQ:PL	0/1:15,13:28:99:264,0,317
-21	10021872	.	T	G	465.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080e+00;ClippingRankSum=-2.073e+00;DP=55;ExcessHet=3.0103;FS=6.604;MLEAC=1;MLEAF=0.500;MQ=22.99;MQRankSum=1.48;QD=8.47;ReadPosRankSum=0.316;SOR=0.193	GT:AD:DP:GQ:PL	0/1:32,23:55:99:473,0,774
-21	10021914	.	C	T	57.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.20;ClippingRankSum=-9.010e-01;DP=76;ExcessHet=3.0103;FS=15.584;MLEAC=1;MLEAF=0.500;MQ=22.32;MQRankSum=-5.170e-01;QD=0.76;ReadPosRankSum=0.281;SOR=3.698	GT:AD:DP:GQ:PL	0/1:65,11:76:65:65,0,1787
-21	10021926	.	T	A	60.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.48;ClippingRankSum=0.696;DP=75;ExcessHet=3.0103;FS=15.617;MLEAC=1;MLEAF=0.500;MQ=22.31;MQRankSum=0.277;QD=0.81;ReadPosRankSum=1.06;SOR=3.742	GT:AD:DP:GQ:PL	0/1:64,11:75:68:68,0,1705
-21	10021968	.	C	T	71.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.040e-01;ClippingRankSum=-6.040e-01;DP=25;ExcessHet=3.0103;FS=12.942;MLEAC=1;MLEAF=0.500;MQ=20.86;MQRankSum=0.159;QD=2.86;ReadPosRankSum=-1.686e+00;SOR=3.909	GT:AD:DP:GQ:PL	0/1:19,6:25:79:79,0,409
-21	10023800	.	C	T	184.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.870e-01;ClippingRankSum=-1.186e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.54;MQRankSum=-8.250e-01;QD=16.78;ReadPosRankSum=-1.031e+00;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,5:11:99:0|1:10023800_C_T:192,0,351
-21	10023808	.	C	G	242.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.52;ClippingRankSum=-1.276e+00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.75;MQRankSum=-1.276e+00;QD=17.33;ReadPosRankSum=-1.276e+00;SOR=1.828	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,7:14:99:0|1:10023800_C_T:250,0,377
-21	10023827	.	G	A	1037.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.25;ClippingRankSum=-1.800e-02;DP=35;ExcessHet=3.0103;FS=5.441;MLEAC=1;MLEAF=0.500;MQ=29.93;MQRankSum=-2.027e+00;QD=29.65;ReadPosRankSum=-2.611e+00;SOR=3.334	GT:AD:DP:GQ:PL	0/1:10,25:35:99:1045,0,208
-21	10023831	.	G	A	682.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.422e+00;ClippingRankSum=-7.870e-01;DP=40;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=29.82;MQRankSum=-1.256e+00;QD=17.07;ReadPosRankSum=-1.891e+00;SOR=2.376	GT:AD:DP:GQ:PL	0/1:16,24:40:99:690,0,658
-21	10023844	.	T	A	1671.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.353;ClippingRankSum=1.12;DP=53;ExcessHet=3.0103;FS=5.781;MLEAC=1;MLEAF=0.500;MQ=30.05;MQRankSum=-3.238e+00;QD=31.54;ReadPosRankSum=0.091;SOR=3.516	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,39:53:99:0|1:10023844_T_A:1679,0,585
-21	10023846	.	A	G	1762.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.613e+00;ClippingRankSum=0.364;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQRankSum=-4.390e+00;QD=32.64;ReadPosRankSum=-4.050e-01;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,41:54:99:0|1:10023844_T_A:1770,0,576
-21	10023849	.	A	G	1765.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.300e+00;ClippingRankSum=-1.000e-02;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.08;MQRankSum=-3.908e+00;QD=30.98;ReadPosRankSum=-3.710e-01;SOR=2.428	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,44:57:99:0|1:10023844_T_A:1773,0,552
-21	10023862	.	A	T	1605.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.330e-01;ClippingRankSum=-5.300e-02;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.01;MQRankSum=-3.496e+00;QD=23.61;ReadPosRankSum=0.038;SOR=2.670	GT:AD:DP:GQ:PL	0/1:14,54:68:99:1613,0,300
-21	10023956	.	G	A	437.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.235;ClippingRankSum=-1.082e+00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.40;MQRankSum=-2.964e+00;QD=15.63;ReadPosRankSum=0.282;SOR=1.179	GT:AD:DP:GQ:PL	0/1:11,17:28:99:445,0,317
-21	10023986	.	C	G	66.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.520e+00;ClippingRankSum=0.678;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.86;MQRankSum=-1.663e+00;QD=6.05;ReadPosRankSum=-1.398e+00;SOR=0.330	GT:AD:DP:GQ:PL	0/1:7,4:11:74:74,0,312
-21	10023990	.	T	C	228.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;ClippingRankSum=-8.950e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.91;MQRankSum=-2.166e+00;QD=22.86;ReadPosRankSum=-1.580e+00;SOR=1.609	GT:AD:DP:GQ:PL	0/1:3,7:10:73:236,0,73
-21	10024210	.	C	T	492.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=-9.190e-01;DP=176;ExcessHet=3.0103;FS=1.624;MLEAC=1;MLEAF=0.500;MQ=31.65;MQRankSum=-1.029e+00;QD=2.80;ReadPosRankSum=1.99;SOR=0.499	GT:AD:DP:GQ:PL	0/1:146,30:176:99:500,0,4486
-21	10024243	.	C	A	118.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.640e-01;ClippingRankSum=0.245;DP=65;ExcessHet=3.0103;FS=7.831;MLEAC=1;MLEAF=0.500;MQ=31.20;MQRankSum=-2.640e-01;QD=1.82;ReadPosRankSum=-1.445e+00;SOR=2.240	GT:AD:DP:GQ:PL	0/1:55,10:65:99:126,0,1587
-21	10024251	.	T	G	148.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.440e-01;ClippingRankSum=-4.800e-02;DP=17;ExcessHet=3.0103;FS=20.434;MLEAC=1;MLEAF=0.500;MQ=25.50;MQRankSum=-2.261e+00;QD=8.74;ReadPosRankSum=-9.140e-01;SOR=4.398	GT:AD:DP:GQ:PL	0/1:9,8:17:99:156,0,232
-21	10024349	.	C	A	43.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.40;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=6.892;MLEAC=1;MLEAF=0.500;MQ=26.62;MQRankSum=-1.479e+00;QD=3.63;ReadPosRankSum=0.185;SOR=2.815	GT:AD:DP:GQ:PL	0/1:9,3:12:51:51,0,240
-21	10024387	.	T	TTG	454.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=-5.640e-01;DP=35;ExcessHet=3.0103;FS=19.313;MLEAC=1;MLEAF=0.500;MQ=31.17;MQRankSum=0.564;QD=15.68;ReadPosRankSum=-4.480e-01;SOR=4.774	GT:AD:DP:GQ:PL	0/1:20,9:32:99:462,0,723
-21	10024422	.	A	G	735.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;ClippingRankSum=-1.630e-01;DP=62;ExcessHet=3.0103;FS=48.917;MLEAC=1;MLEAF=0.500;MQ=34.53;MQRankSum=-1.450e+00;QD=11.86;ReadPosRankSum=0.361;SOR=6.514	GT:AD:DP:GQ:PL	0/1:34,28:62:99:743,0,984
-21	10024476	.	A	T	1794.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920e-01;ClippingRankSum=-3.340e-01;DP=95;ExcessHet=3.0103;FS=82.650;MLEAC=1;MLEAF=0.500;MQ=35.84;MQRankSum=-2.949e+00;QD=20.63;ReadPosRankSum=1.07;SOR=7.736	GT:AD:DP:GQ:PL	0/1:41,46:95:99:1802,0,1557
-21	10024499	.	G	C	1438.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.33;ClippingRankSum=-1.400e-02;DP=80;ExcessHet=3.0103;FS=49.164;MLEAC=1;MLEAF=0.500;MQ=34.17;MQRankSum=-6.980e-01;QD=17.98;ReadPosRankSum=2.82;SOR=6.458	GT:AD:DP:GQ:PL	0/1:40,40:80:99:1446,0,1481
-21	10024500	.	C	T	1866.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.28;ClippingRankSum=-2.242e+00;DP=79;ExcessHet=3.0103;FS=67.159;MLEAC=1;MLEAF=0.500;MQ=34.23;MQRankSum=-1.148e+00;QD=23.63;ReadPosRankSum=2.66;SOR=7.357	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,46:79:99:0|1:10024500_C_T:1874,0,1244
-21	10024509	.	G	A	704.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;ClippingRankSum=-1.800e-01;DP=71;ExcessHet=3.0103;FS=18.563;MLEAC=1;MLEAF=0.500;MQ=34.46;MQRankSum=-5.160e-01;QD=9.92;ReadPosRankSum=0.106;SOR=3.933	GT:AD:DP:GQ:PGT:PID:PL	0/1:49,22:71:99:0|1:10024509_G_A:712,0,1999
-21	10024511	.	G	A	1668.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.104e+00;ClippingRankSum=1.11;DP=67;ExcessHet=3.0103;FS=47.770;MLEAC=1;MLEAF=0.500;MQ=34.36;MQRankSum=-6.000e-03;QD=24.90;ReadPosRankSum=1.16;SOR=6.568	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,39:67:99:0|1:10024500_C_T:1676,0,1091
-21	10024526	.	T	C	1431.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.113e+00;ClippingRankSum=-6.040e-01;DP=57;ExcessHet=3.0103;FS=44.858;MLEAC=1;MLEAF=0.500;MQ=33.27;MQRankSum=0.290;QD=25.12;ReadPosRankSum=-9.020e-01;SOR=6.698	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,36:57:99:0|1:10024500_C_T:1439,0,899
-21	10024531	.	G	C	600.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.05;ClippingRankSum=0.389;DP=50;ExcessHet=3.0103;FS=10.982;MLEAC=1;MLEAF=0.500;MQ=32.64;MQRankSum=-2.050e-01;QD=12.01;ReadPosRankSum=-2.580e+00;SOR=3.383	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,17:50:99:0|1:10024509_G_A:608,0,1418
-21	10024550	.	G	A	526.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.50;ClippingRankSum=-5.400e-01;DP=31;ExcessHet=3.0103;FS=16.108;MLEAC=1;MLEAF=0.500;MQ=32.42;MQRankSum=1.54;QD=16.99;ReadPosRankSum=-9.410e-01;SOR=4.479	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,13:31:99:0|1:10024500_C_T:534,0,641
-21	10024975	.	T	C	147.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.078e+00;ClippingRankSum=-2.900e-02;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.64;MQRankSum=-7.280e-01;QD=5.90;ReadPosRankSum=-7.280e-01;SOR=1.038	GT:AD:DP:GQ:PL	0/1:17,8:25:99:155,0,403
-21	10026444	.	A	T	433.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.548e+00;ClippingRankSum=-2.002e+00;DP=31;ExcessHet=3.0103;FS=5.697;MLEAC=1;MLEAF=0.500;MQ=28.16;MQRankSum=1.30;QD=13.99;ReadPosRankSum=2.13;SOR=2.599	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,11:31:99:0|1:10026444_A_T:441,0,822
-21	10026447	.	G	T	430.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.994;ClippingRankSum=0.223;DP=31;ExcessHet=3.0103;FS=8.572;MLEAC=1;MLEAF=0.500;MQ=28.37;MQRankSum=0.142;QD=13.89;ReadPosRankSum=1.93;SOR=2.862	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,12:31:99:0|1:10026444_A_T:438,0,852
-21	10026450	.	A	T	446.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.561e+00;ClippingRankSum=0.142;DP=31;ExcessHet=3.0103;FS=5.775;MLEAC=1;MLEAF=0.500;MQ=28.07;MQRankSum=0.912;QD=14.41;ReadPosRankSum=2.13;SOR=2.338	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,12:31:99:0|1:10026444_A_T:454,0,748
-21	10026475	.	G	A	180.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.664;ClippingRankSum=-1.500e-02;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.84;MQRankSum=-4.280e-01;QD=4.30;ReadPosRankSum=1.67;SOR=0.105	GT:AD:DP:GQ:PL	0/1:32,10:42:99:188,0,1086
-21	10026503	.	G	C	188.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.205e+00;ClippingRankSum=0.618;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=0.388;QD=4.39;ReadPosRankSum=-1.912e+00;SOR=0.100	GT:AD:DP:GQ:PL	0/1:33,10:43:99:196,0,1300
-21	10026515	.	A	T	628.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.598e+00;ClippingRankSum=-1.172e+00;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.86;MQRankSum=-9.230e-01;QD=12.83;ReadPosRankSum=-9.300e-02;SOR=0.917	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,18:49:99:0|1:10026515_A_T:636,0,1227
-21	10026528	.	C	A	439.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=0.826;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.94;MQRankSum=-8.530e-01;QD=10.22;ReadPosRankSum=1.12;SOR=0.990	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,12:43:99:0|1:10026515_A_T:447,0,1318
-21	10026531	.	C	T	406.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=-1.920e-01;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.93;MQRankSum=-8.120e-01;QD=10.17;ReadPosRankSum=0.546;SOR=1.127	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,12:40:99:0|1:10026515_A_T:414,0,1195
-21	10026539	.	A	T	910.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.60;ClippingRankSum=0.715;DP=39;ExcessHet=3.0103;FS=10.503;MLEAC=1;MLEAF=0.500;MQ=29.13;MQRankSum=-2.590e-01;QD=23.35;ReadPosRankSum=1.17;SOR=4.083	GT:AD:DP:GQ:PL	0/1:12,27:39:99:918,0,291
-21	10026560	.	G	A	167.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;ClippingRankSum=0.418;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.14;MQRankSum=0.242;QD=5.08;ReadPosRankSum=-4.180e-01;SOR=0.653	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,7:33:99:0|1:10026560_G_A:175,0,1051
-21	10026569	.	T	G	285.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.337;ClippingRankSum=0.214;DP=24;ExcessHet=3.0103;FS=2.706;MLEAC=1;MLEAF=0.500;MQ=28.69;MQRankSum=1.07;QD=11.90;ReadPosRankSum=-1.010e+00;SOR=1.445	GT:AD:DP:GQ:PL	0/1:16,8:24:99:293,0,492
-21	10026573	.	A	T	100.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.900e-02;ClippingRankSum=0.891;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.69;MQRankSum=0.503;QD=4.19;ReadPosRankSum=-5.810e-01;SOR=0.484	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,4:24:99:0|1:10026560_G_A:108,0,828
-21	10026576	.	G	C	100.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393e+00;ClippingRankSum=2.56;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.68;MQRankSum=0.041;QD=4.37;ReadPosRankSum=-1.095e+00;SOR=0.527	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,4:23:99:0|1:10026560_G_A:108,0,828
-21	10026594	.	T	C	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.850e+00;ClippingRankSum=0.150;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.61;MQRankSum=1.25;QD=3.56;ReadPosRankSum=1.35;SOR=0.765	GT:AD:DP:GQ:PL	0/1:15,4:19:75:75,0,529
-21	10026748	.	A	G	271.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.419e+00;ClippingRankSum=-1.684e+00;DP=24;ExcessHet=3.0103;FS=4.117;MLEAC=1;MLEAF=0.500;MQ=32.43;MQRankSum=-6.430e-01;QD=11.32;ReadPosRankSum=0.031;SOR=1.863	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,8:24:99:0|1:10026748_A_G:279,0,744
-21	10026762	.	C	T	291.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.12;ClippingRankSum=0.519;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.09;MQRankSum=-1.185e+00;QD=6.34;ReadPosRankSum=1.37;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,10:46:99:0|1:10026748_A_G:299,0,1348
-21	10026809	.	A	G	540.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.934e+00;ClippingRankSum=-8.980e-01;DP=114;ExcessHet=3.0103;FS=4.863;MLEAC=1;MLEAF=0.500;MQ=35.31;MQRankSum=0.913;QD=4.74;ReadPosRankSum=-2.640e-01;SOR=1.340	GT:AD:DP:GQ:PGT:PID:PL	0/1:94,20:114:99:0|1:10026809_A_G:548,0,3991
-21	10026826	.	T	C	513.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.024e+00;ClippingRankSum=-3.500e-01;DP=122;ExcessHet=3.0103;FS=1.743;MLEAC=1;MLEAF=0.500;MQ=35.57;MQRankSum=-4.575e+00;QD=4.21;ReadPosRankSum=2.89;SOR=0.506	GT:AD:DP:GQ:PL	0/1:94,28:122:99:521,0,3516
-21	10026829	.	A	C	554.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.797e+00;ClippingRankSum=0.495;DP=122;ExcessHet=3.0103;FS=3.202;MLEAC=1;MLEAF=0.500;MQ=35.57;MQRankSum=1.76;QD=4.55;ReadPosRankSum=-1.120e+00;SOR=1.096	GT:AD:DP:GQ:PGT:PID:PL	0/1:101,21:122:99:0|1:10026809_A_G:562,0,4131
-21	10026848	.	C	T	213.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.840e-01;ClippingRankSum=-1.211e+00;DP=102;ExcessHet=3.0103;FS=2.381;MLEAC=1;MLEAF=0.500;MQ=35.60;MQRankSum=2.08;QD=2.09;ReadPosRankSum=2.01;SOR=0.428	GT:AD:DP:GQ:PL	0/1:88,14:102:99:221,0,3483
-21	10026857	.	C	T	715.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.98;ClippingRankSum=0.104;DP=89;ExcessHet=3.0103;FS=0.909;MLEAC=1;MLEAF=0.500;MQ=35.50;MQRankSum=-4.940e+00;QD=8.04;ReadPosRankSum=-1.836e+00;SOR=0.892	GT:AD:DP:GQ:PL	0/1:63,26:89:99:723,0,2361
-21	10026865	.	C	T	102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=0.549;DP=82;ExcessHet=3.0103;FS=1.404;MLEAC=1;MLEAF=0.500;MQ=35.20;MQRankSum=0.653;QD=1.25;ReadPosRankSum=0.935;SOR=0.413	GT:AD:DP:GQ:PL	0/1:73,9:82:99:110,0,2726
-21	10026877	.	G	A	101.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.56;ClippingRankSum=0.596;DP=56;ExcessHet=3.0103;FS=1.668;MLEAC=1;MLEAF=0.500;MQ=34.09;MQRankSum=-2.318e+00;QD=1.81;ReadPosRankSum=-2.159e+00;SOR=0.378	GT:AD:DP:GQ:PL	0/1:50,6:56:99:109,0,2122
-21	10027057	.	G	T	39.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.208e+00;ClippingRankSum=0.149;DP=103;ExcessHet=3.0103;FS=21.387;MLEAC=1;MLEAF=0.500;MQ=29.06;MQRankSum=-1.331e+00;QD=0.38;ReadPosRankSum=1.01;SOR=4.314	GT:AD:DP:GQ:PL	0/1:91,12:103:47:47,0,2804
-21	10027130	.	A	C	165.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.371;ClippingRankSum=0.801;DP=78;ExcessHet=3.0103;FS=28.095;MLEAC=1;MLEAF=0.500;MQ=33.21;MQRankSum=-1.283e+00;QD=2.12;ReadPosRankSum=1.01;SOR=4.813	GT:AD:DP:GQ:PL	0/1:64,14:78:99:173,0,2324
-21	10027140	.	T	C	1169.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.780e-01;ClippingRankSum=-2.650e-01;DP=70;ExcessHet=3.0103;FS=30.059;MLEAC=1;MLEAF=0.500;MQ=33.84;MQRankSum=-2.199e+00;QD=16.71;ReadPosRankSum=-1.350e+00;SOR=3.682	GT:AD:DP:GQ:PL	0/1:32,38:70:99:1177,0,912
-21	10027153	.	G	T	220.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.19;ClippingRankSum=-1.000e-01;DP=58;ExcessHet=3.0103;FS=25.663;MLEAC=1;MLEAF=0.500;MQ=33.27;MQRankSum=-1.336e+00;QD=3.80;ReadPosRankSum=-1.730e-01;SOR=4.722	GT:AD:DP:GQ:PL	0/1:44,14:58:99:228,0,1259
-21	10027583	.	G	A	50.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.218e+00;ClippingRankSum=-1.300e-01;DP=31;ExcessHet=3.0103;FS=1.958;MLEAC=1;MLEAF=0.500;MQ=26.35;MQRankSum=0.233;QD=1.69;ReadPosRankSum=0.078;SOR=1.259	GT:AD:DP:GQ:PL	0/1:24,6:30:58:58,0,594
-21	10027880	.	C	T	166.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;ClippingRankSum=0.141;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.66;MQRankSum=-1.065e+00;QD=3.70;ReadPosRankSum=1.32;SOR=0.638	GT:AD:DP:GQ:PL	0/1:33,12:45:99:174,0,710
-21	10028325	.	C	A	137.93	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.69;QD=22.99;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,6:6:18:152,18,0
-21	10029217	.	G	A	34.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=1.03;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.10;MQRankSum=1.03;QD=8.65;ReadPosRankSum=-1.026e+00;SOR=0.105	GT:AD:DP:GQ:PL	0/1:2,2:4:40:42,0,40
-21	10029407	.	A	G	124.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.230e-01;ClippingRankSum=-1.203e+00;DP=46;ExcessHet=3.0103;FS=21.891;MLEAC=1;MLEAF=0.500;MQ=37.52;MQRankSum=-4.780e-01;QD=2.71;ReadPosRankSum=-2.391e+00;SOR=4.405	GT:AD:DP:GQ:PL	0/1:38,8:46:99:132,0,1203
-21	10029437	.	A	G	84.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.147e+00;ClippingRankSum=-1.459e+00;DP=57;ExcessHet=3.0103;FS=13.341;MLEAC=1;MLEAF=0.500;MQ=36.58;MQRankSum=-3.560e-01;QD=1.48;ReadPosRankSum=0.310;SOR=3.386	GT:AD:DP:GQ:PL	0/1:49,8:57:92:92,0,1568
-21	10030170	.	C	G	58.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.600e-02;ClippingRankSum=-4.600e-02;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.37;MQRankSum=-1.871e+00;QD=2.55;ReadPosRankSum=1.05;SOR=0.036	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,3:23:66:0|1:10030170_C_G:66,0,980
-21	10030177	.	C	T	61.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.66;ClippingRankSum=0.151;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.53;MQRankSum=-1.759e+00;QD=2.93;ReadPosRankSum=0.352;SOR=0.043	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,3:21:69:0|1:10030170_C_G:69,0,945
-21	10031838	.	T	C	194.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.130e-01;ClippingRankSum=-8.720e-01;DP=21;ExcessHet=3.0103;FS=4.834;MLEAC=1;MLEAF=0.500;MQ=29.87;MQRankSum=2.06;QD=9.73;ReadPosRankSum=-2.694e+00;SOR=2.340	GT:AD:DP:GQ:PL	0/1:13,7:20:99:202,0,417
-21	10031861	.	C	A	95.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.18;ClippingRankSum=1.42;DP=32;ExcessHet=3.0103;FS=17.171;MLEAC=1;MLEAF=0.500;MQ=28.35;MQRankSum=1.52;QD=2.99;ReadPosRankSum=3.31;SOR=3.903	GT:AD:DP:GQ:PL	0/1:26,6:32:99:103,0,818
+21	10020798	.	G	A	810.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.61;ClippingRankSum=0.094;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.61;MQRankSum=-4.325e+00;QD=10.67;ReadPosRankSum=1.78;SOR=0.585	GT:AD:DP:GQ:PL	0/1:41,35:76:99:818,0,1128
+21	10020975	.	G	A	145.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=0.590;DP=54;ExcessHet=3.0103;FS=16.658;MLEAC=1;MLEAF=0.500;MQ=32.05;MQRankSum=0.189;QD=2.70;ReadPosRankSum=-6.350e-01;SOR=3.932	GT:AD:DP:GQ:PL	0/1:44,10:54:99:153,0,1192
+21	10021000	.	T	G	369.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.840e-01;ClippingRankSum=1.21;DP=56;ExcessHet=3.0103;FS=22.753;MLEAC=1;MLEAF=0.500;MQ=27.64;MQRankSum=1.23;QD=6.60;ReadPosRankSum=0.499;SOR=4.690	GT:AD:DP:GQ:PL	0/1:39,17:56:99:377,0,1010
+21	10021012	.	C	T	368.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.17;ClippingRankSum=0.017;DP=58;ExcessHet=3.0103;FS=21.916;MLEAC=1;MLEAF=0.500;MQ=27.95;MQRankSum=1.55;QD=6.36;ReadPosRankSum=2.13;SOR=4.337	GT:AD:DP:GQ:PL	0/1:41,17:58:99:376,0,1101
+21	10021100	.	C	A	128.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.900e-02;ClippingRankSum=0.147;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.56;MQRankSum=-3.430e-01;QD=4.29;ReadPosRankSum=-4.900e-01;SOR=0.395	GT:AD:DP:GQ:PL	0/1:23,7:30:99:136,0,703
+21	10021586	.	G	T	256.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.15;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=5.590;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=-3.690e-01;QD=9.17;ReadPosRankSum=2.26;SOR=1.567	GT:AD:DP:GQ:PL	0/1:15,13:28:99:264,0,317
+21	10021872	.	T	G	465.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080e+00;ClippingRankSum=-2.073e+00;DP=55;ExcessHet=3.0103;FS=6.604;MLEAC=1;MLEAF=0.500;MQ=22.99;MQRankSum=1.48;QD=8.47;ReadPosRankSum=0.316;SOR=0.193	GT:AD:DP:GQ:PL	0/1:32,23:55:99:473,0,774
+21	10021914	.	C	T	57.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.20;ClippingRankSum=-9.010e-01;DP=76;ExcessHet=3.0103;FS=15.584;MLEAC=1;MLEAF=0.500;MQ=22.32;MQRankSum=-5.170e-01;QD=0.76;ReadPosRankSum=0.281;SOR=3.698	GT:AD:DP:GQ:PL	0/1:65,11:76:65:65,0,1787
+21	10021926	.	T	A	60.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.48;ClippingRankSum=0.696;DP=75;ExcessHet=3.0103;FS=15.617;MLEAC=1;MLEAF=0.500;MQ=22.31;MQRankSum=0.277;QD=0.81;ReadPosRankSum=1.06;SOR=3.742	GT:AD:DP:GQ:PL	0/1:64,11:75:68:68,0,1705
+21	10021968	.	C	T	71.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.040e-01;ClippingRankSum=-6.040e-01;DP=25;ExcessHet=3.0103;FS=12.942;MLEAC=1;MLEAF=0.500;MQ=20.86;MQRankSum=0.159;QD=2.87;ReadPosRankSum=-1.686e+00;SOR=3.909	GT:AD:DP:GQ:PL	0/1:19,6:25:79:79,0,409
+21	10023800	.	C	T	184.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.870e-01;ClippingRankSum=-1.186e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.54;MQRankSum=-8.250e-01;QD=16.79;ReadPosRankSum=-1.031e+00;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,5:11:99:0|1:10023800_C_T:192,0,351
+21	10023808	.	C	G	242.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.52;ClippingRankSum=-1.276e+00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.75;MQRankSum=-1.276e+00;QD=17.33;ReadPosRankSum=-1.276e+00;SOR=1.828	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,7:14:99:0|1:10023800_C_T:250,0,377
+21	10023827	.	G	A	1037.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.25;ClippingRankSum=-1.800e-02;DP=35;ExcessHet=3.0103;FS=5.441;MLEAC=1;MLEAF=0.500;MQ=29.93;MQRankSum=-2.027e+00;QD=29.65;ReadPosRankSum=-2.611e+00;SOR=3.334	GT:AD:DP:GQ:PL	0/1:10,25:35:99:1045,0,208
+21	10023831	.	G	A	682.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.422e+00;ClippingRankSum=-7.870e-01;DP=40;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=29.82;MQRankSum=-1.256e+00;QD=17.07;ReadPosRankSum=-1.891e+00;SOR=2.376	GT:AD:DP:GQ:PL	0/1:16,24:40:99:690,0,658
+21	10023844	.	T	A	1671.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.353;ClippingRankSum=1.12;DP=53;ExcessHet=3.0103;FS=5.781;MLEAC=1;MLEAF=0.500;MQ=30.05;MQRankSum=-3.238e+00;QD=31.54;ReadPosRankSum=0.091;SOR=3.516	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,39:53:99:0|1:10023844_T_A:1679,0,585
+21	10023846	.	A	G	1762.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.613e+00;ClippingRankSum=0.364;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQRankSum=-4.390e+00;QD=32.64;ReadPosRankSum=-4.050e-01;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,41:54:99:0|1:10023844_T_A:1770,0,576
+21	10023849	.	A	G	1765.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.300e+00;ClippingRankSum=-1.000e-02;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.08;MQRankSum=-3.908e+00;QD=30.98;ReadPosRankSum=-3.710e-01;SOR=2.428	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,44:57:99:0|1:10023844_T_A:1773,0,552
+21	10023862	.	A	T	1605.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.330e-01;ClippingRankSum=-5.300e-02;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.01;MQRankSum=-3.496e+00;QD=23.61;ReadPosRankSum=0.038;SOR=2.670	GT:AD:DP:GQ:PL	0/1:14,54:68:99:1613,0,300
+21	10023956	.	G	A	437.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.235;ClippingRankSum=-1.082e+00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.40;MQRankSum=-2.964e+00;QD=15.63;ReadPosRankSum=0.282;SOR=1.179	GT:AD:DP:GQ:PL	0/1:11,17:28:99:445,0,317
+21	10023986	.	C	G	66.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.520e+00;ClippingRankSum=0.678;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.86;MQRankSum=-1.663e+00;QD=6.06;ReadPosRankSum=-1.398e+00;SOR=0.330	GT:AD:DP:GQ:PL	0/1:7,4:11:74:74,0,312
+21	10023990	.	T	C	228.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;ClippingRankSum=-8.950e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.91;MQRankSum=-2.166e+00;QD=22.86;ReadPosRankSum=-1.580e+00;SOR=1.609	GT:AD:DP:GQ:PL	0/1:3,7:10:73:236,0,73
+21	10024210	.	C	T	492.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=-9.190e-01;DP=176;ExcessHet=3.0103;FS=1.624;MLEAC=1;MLEAF=0.500;MQ=31.65;MQRankSum=-1.029e+00;QD=2.80;ReadPosRankSum=1.99;SOR=0.499	GT:AD:DP:GQ:PL	0/1:146,30:176:99:500,0,4486
+21	10024243	.	C	A	118.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.640e-01;ClippingRankSum=0.245;DP=65;ExcessHet=3.0103;FS=7.831;MLEAC=1;MLEAF=0.500;MQ=31.20;MQRankSum=-2.640e-01;QD=1.83;ReadPosRankSum=-1.445e+00;SOR=2.240	GT:AD:DP:GQ:PL	0/1:55,10:65:99:126,0,1587
+21	10024251	.	T	G	148.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.440e-01;ClippingRankSum=-4.800e-02;DP=17;ExcessHet=3.0103;FS=20.434;MLEAC=1;MLEAF=0.500;MQ=25.50;MQRankSum=-2.261e+00;QD=8.74;ReadPosRankSum=-9.140e-01;SOR=4.398	GT:AD:DP:GQ:PL	0/1:9,8:17:99:156,0,232
+21	10024349	.	C	A	43.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.40;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=6.892;MLEAC=1;MLEAF=0.500;MQ=26.62;MQRankSum=-1.479e+00;QD=3.64;ReadPosRankSum=0.185;SOR=2.815	GT:AD:DP:GQ:PL	0/1:9,3:12:51:51,0,240
+21	10024387	.	T	TTG	454.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=-5.640e-01;DP=35;ExcessHet=3.0103;FS=19.313;MLEAC=1;MLEAF=0.500;MQ=31.17;MQRankSum=0.564;QD=15.68;ReadPosRankSum=-4.480e-01;SOR=4.774	GT:AD:DP:GQ:PL	0/1:20,9:32:99:462,0,723
+21	10024422	.	A	G	735.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;ClippingRankSum=-1.630e-01;DP=62;ExcessHet=3.0103;FS=48.917;MLEAC=1;MLEAF=0.500;MQ=34.53;MQRankSum=-1.450e+00;QD=11.87;ReadPosRankSum=0.361;SOR=6.514	GT:AD:DP:GQ:PL	0/1:34,28:62:99:743,0,984
+21	10024476	.	A	T	1794.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920e-01;ClippingRankSum=-3.340e-01;DP=95;ExcessHet=3.0103;FS=82.650;MLEAC=1;MLEAF=0.500;MQ=35.84;MQRankSum=-2.949e+00;QD=20.63;ReadPosRankSum=1.07;SOR=7.736	GT:AD:DP:GQ:PL	0/1:41,46:95:99:1802,0,1557
+21	10024499	.	G	C	1438.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.33;ClippingRankSum=-1.400e-02;DP=80;ExcessHet=3.0103;FS=49.164;MLEAC=1;MLEAF=0.500;MQ=34.17;MQRankSum=-6.980e-01;QD=17.98;ReadPosRankSum=2.82;SOR=6.458	GT:AD:DP:GQ:PL	0/1:40,40:80:99:1446,0,1481
+21	10024500	.	C	T	1866.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.28;ClippingRankSum=-2.242e+00;DP=79;ExcessHet=3.0103;FS=67.159;MLEAC=1;MLEAF=0.500;MQ=34.23;MQRankSum=-1.148e+00;QD=23.63;ReadPosRankSum=2.66;SOR=7.357	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,46:79:99:0|1:10024500_C_T:1874,0,1244
+21	10024509	.	G	A	704.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;ClippingRankSum=-1.800e-01;DP=71;ExcessHet=3.0103;FS=18.563;MLEAC=1;MLEAF=0.500;MQ=34.46;MQRankSum=-5.160e-01;QD=9.92;ReadPosRankSum=0.106;SOR=3.933	GT:AD:DP:GQ:PGT:PID:PL	0/1:49,22:71:99:0|1:10024509_G_A:712,0,1999
+21	10024511	.	G	A	1668.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.104e+00;ClippingRankSum=1.11;DP=67;ExcessHet=3.0103;FS=47.770;MLEAC=1;MLEAF=0.500;MQ=34.36;MQRankSum=-6.000e-03;QD=24.91;ReadPosRankSum=1.16;SOR=6.568	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,39:67:99:0|1:10024500_C_T:1676,0,1091
+21	10024526	.	T	C	1431.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.113e+00;ClippingRankSum=-6.040e-01;DP=57;ExcessHet=3.0103;FS=44.858;MLEAC=1;MLEAF=0.500;MQ=33.27;MQRankSum=0.290;QD=25.12;ReadPosRankSum=-9.020e-01;SOR=6.698	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,36:57:99:0|1:10024500_C_T:1439,0,899
+21	10024531	.	G	C	600.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.05;ClippingRankSum=0.389;DP=50;ExcessHet=3.0103;FS=10.982;MLEAC=1;MLEAF=0.500;MQ=32.64;MQRankSum=-2.050e-01;QD=12.01;ReadPosRankSum=-2.580e+00;SOR=3.383	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,17:50:99:0|1:10024509_G_A:608,0,1418
+21	10024550	.	G	A	526.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.50;ClippingRankSum=-5.400e-01;DP=31;ExcessHet=3.0103;FS=16.108;MLEAC=1;MLEAF=0.500;MQ=32.42;MQRankSum=1.54;QD=16.99;ReadPosRankSum=-9.410e-01;SOR=4.479	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,13:31:99:0|1:10024500_C_T:534,0,641
+21	10024975	.	T	C	147.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.078e+00;ClippingRankSum=-2.900e-02;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.64;MQRankSum=-7.280e-01;QD=5.91;ReadPosRankSum=-7.280e-01;SOR=1.038	GT:AD:DP:GQ:PL	0/1:17,8:25:99:155,0,403
+21	10026444	.	A	T	433.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.548e+00;ClippingRankSum=-2.002e+00;DP=31;ExcessHet=3.0103;FS=5.697;MLEAC=1;MLEAF=0.500;MQ=28.16;MQRankSum=1.30;QD=13.99;ReadPosRankSum=2.13;SOR=2.599	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,11:31:99:0|1:10026444_A_T:441,0,822
+21	10026447	.	G	T	430.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.994;ClippingRankSum=0.223;DP=31;ExcessHet=3.0103;FS=8.572;MLEAC=1;MLEAF=0.500;MQ=28.37;MQRankSum=0.142;QD=13.89;ReadPosRankSum=1.93;SOR=2.862	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,12:31:99:0|1:10026444_A_T:438,0,852
+21	10026450	.	A	T	446.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.561e+00;ClippingRankSum=0.142;DP=31;ExcessHet=3.0103;FS=5.775;MLEAC=1;MLEAF=0.500;MQ=28.07;MQRankSum=0.912;QD=14.41;ReadPosRankSum=2.13;SOR=2.338	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,12:31:99:0|1:10026444_A_T:454,0,748
+21	10026475	.	G	A	180.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.664;ClippingRankSum=-1.500e-02;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.84;MQRankSum=-4.280e-01;QD=4.30;ReadPosRankSum=1.67;SOR=0.105	GT:AD:DP:GQ:PL	0/1:32,10:42:99:188,0,1086
+21	10026503	.	G	C	188.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.205e+00;ClippingRankSum=0.618;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=0.388;QD=4.39;ReadPosRankSum=-1.912e+00;SOR=0.100	GT:AD:DP:GQ:PL	0/1:33,10:43:99:196,0,1300
+21	10026515	.	A	T	628.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.598e+00;ClippingRankSum=-1.172e+00;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.86;MQRankSum=-9.230e-01;QD=12.83;ReadPosRankSum=-9.300e-02;SOR=0.917	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,18:49:99:0|1:10026515_A_T:636,0,1227
+21	10026528	.	C	A	439.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=0.826;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.94;MQRankSum=-8.530e-01;QD=10.22;ReadPosRankSum=1.12;SOR=0.990	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,12:43:99:0|1:10026515_A_T:447,0,1318
+21	10026531	.	C	T	406.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=-1.920e-01;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.93;MQRankSum=-8.120e-01;QD=10.17;ReadPosRankSum=0.546;SOR=1.127	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,12:40:99:0|1:10026515_A_T:414,0,1195
+21	10026539	.	A	T	910.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.60;ClippingRankSum=0.715;DP=39;ExcessHet=3.0103;FS=10.503;MLEAC=1;MLEAF=0.500;MQ=29.13;MQRankSum=-2.590e-01;QD=23.35;ReadPosRankSum=1.17;SOR=4.083	GT:AD:DP:GQ:PL	0/1:12,27:39:99:918,0,291
+21	10026560	.	G	A	167.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;ClippingRankSum=0.418;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.14;MQRankSum=0.242;QD=5.08;ReadPosRankSum=-4.180e-01;SOR=0.653	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,7:33:99:0|1:10026560_G_A:175,0,1051
+21	10026569	.	T	G	285.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.337;ClippingRankSum=0.214;DP=24;ExcessHet=3.0103;FS=2.706;MLEAC=1;MLEAF=0.500;MQ=28.69;MQRankSum=1.07;QD=11.90;ReadPosRankSum=-1.010e+00;SOR=1.445	GT:AD:DP:GQ:PL	0/1:16,8:24:99:293,0,492
+21	10026573	.	A	T	100.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.900e-02;ClippingRankSum=0.891;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.69;MQRankSum=0.503;QD=4.19;ReadPosRankSum=-5.810e-01;SOR=0.484	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,4:24:99:0|1:10026560_G_A:108,0,828
+21	10026576	.	G	C	100.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393e+00;ClippingRankSum=2.56;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.68;MQRankSum=0.041;QD=4.38;ReadPosRankSum=-1.095e+00;SOR=0.527	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,4:23:99:0|1:10026560_G_A:108,0,828
+21	10026594	.	T	C	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.850e+00;ClippingRankSum=0.150;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.61;MQRankSum=1.25;QD=3.56;ReadPosRankSum=1.35;SOR=0.765	GT:AD:DP:GQ:PL	0/1:15,4:19:75:75,0,529
+21	10026748	.	A	G	271.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.419e+00;ClippingRankSum=-1.684e+00;DP=24;ExcessHet=3.0103;FS=4.117;MLEAC=1;MLEAF=0.500;MQ=32.43;MQRankSum=-6.430e-01;QD=11.32;ReadPosRankSum=0.031;SOR=1.863	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,8:24:99:0|1:10026748_A_G:279,0,744
+21	10026762	.	C	T	291.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.12;ClippingRankSum=0.519;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.09;MQRankSum=-1.185e+00;QD=6.34;ReadPosRankSum=1.37;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,10:46:99:0|1:10026748_A_G:299,0,1348
+21	10026809	.	A	G	540.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.934e+00;ClippingRankSum=-8.980e-01;DP=114;ExcessHet=3.0103;FS=4.863;MLEAC=1;MLEAF=0.500;MQ=35.31;MQRankSum=0.913;QD=4.74;ReadPosRankSum=-2.640e-01;SOR=1.340	GT:AD:DP:GQ:PGT:PID:PL	0/1:94,20:114:99:0|1:10026809_A_G:548,0,3991
+21	10026826	.	T	C	513.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.024e+00;ClippingRankSum=-3.500e-01;DP=122;ExcessHet=3.0103;FS=1.743;MLEAC=1;MLEAF=0.500;MQ=35.57;MQRankSum=-4.575e+00;QD=4.21;ReadPosRankSum=2.89;SOR=0.506	GT:AD:DP:GQ:PL	0/1:94,28:122:99:521,0,3516
+21	10026829	.	A	C	554.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.797e+00;ClippingRankSum=0.495;DP=122;ExcessHet=3.0103;FS=3.202;MLEAC=1;MLEAF=0.500;MQ=35.57;MQRankSum=1.76;QD=4.55;ReadPosRankSum=-1.120e+00;SOR=1.096	GT:AD:DP:GQ:PGT:PID:PL	0/1:101,21:122:99:0|1:10026809_A_G:562,0,4131
+21	10026848	.	C	T	213.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.840e-01;ClippingRankSum=-1.211e+00;DP=102;ExcessHet=3.0103;FS=2.381;MLEAC=1;MLEAF=0.500;MQ=35.60;MQRankSum=2.08;QD=2.09;ReadPosRankSum=2.01;SOR=0.428	GT:AD:DP:GQ:PL	0/1:88,14:102:99:221,0,3483
+21	10026857	.	C	T	715.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.98;ClippingRankSum=0.104;DP=89;ExcessHet=3.0103;FS=0.909;MLEAC=1;MLEAF=0.500;MQ=35.50;MQRankSum=-4.940e+00;QD=8.04;ReadPosRankSum=-1.836e+00;SOR=0.892	GT:AD:DP:GQ:PL	0/1:63,26:89:99:723,0,2361
+21	10026865	.	C	T	102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=0.549;DP=82;ExcessHet=3.0103;FS=1.404;MLEAC=1;MLEAF=0.500;MQ=35.20;MQRankSum=0.653;QD=1.25;ReadPosRankSum=0.935;SOR=0.413	GT:AD:DP:GQ:PL	0/1:73,9:82:99:110,0,2726
+21	10026877	.	G	A	101.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.56;ClippingRankSum=0.596;DP=56;ExcessHet=3.0103;FS=1.668;MLEAC=1;MLEAF=0.500;MQ=34.09;MQRankSum=-2.318e+00;QD=1.81;ReadPosRankSum=-2.159e+00;SOR=0.378	GT:AD:DP:GQ:PL	0/1:50,6:56:99:109,0,2122
+21	10027057	.	G	T	39.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.208e+00;ClippingRankSum=0.149;DP=103;ExcessHet=3.0103;FS=21.387;MLEAC=1;MLEAF=0.500;MQ=29.06;MQRankSum=-1.331e+00;QD=0.38;ReadPosRankSum=1.01;SOR=4.314	GT:AD:DP:GQ:PL	0/1:91,12:103:47:47,0,2804
+21	10027130	.	A	C	165.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.371;ClippingRankSum=0.801;DP=78;ExcessHet=3.0103;FS=28.095;MLEAC=1;MLEAF=0.500;MQ=33.21;MQRankSum=-1.283e+00;QD=2.12;ReadPosRankSum=1.01;SOR=4.813	GT:AD:DP:GQ:PL	0/1:64,14:78:99:173,0,2324
+21	10027140	.	T	C	1169.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.780e-01;ClippingRankSum=-2.650e-01;DP=70;ExcessHet=3.0103;FS=30.059;MLEAC=1;MLEAF=0.500;MQ=33.84;MQRankSum=-2.199e+00;QD=16.71;ReadPosRankSum=-1.350e+00;SOR=3.682	GT:AD:DP:GQ:PL	0/1:32,38:70:99:1177,0,912
+21	10027153	.	G	T	220.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.19;ClippingRankSum=-1.000e-01;DP=58;ExcessHet=3.0103;FS=25.663;MLEAC=1;MLEAF=0.500;MQ=33.27;MQRankSum=-1.336e+00;QD=3.80;ReadPosRankSum=-1.730e-01;SOR=4.722	GT:AD:DP:GQ:PL	0/1:44,14:58:99:228,0,1259
+21	10027583	.	G	A	50.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.218e+00;ClippingRankSum=-1.300e-01;DP=31;ExcessHet=3.0103;FS=1.958;MLEAC=1;MLEAF=0.500;MQ=26.35;MQRankSum=0.233;QD=1.69;ReadPosRankSum=0.078;SOR=1.259	GT:AD:DP:GQ:PL	0/1:24,6:30:58:58,0,594
+21	10027880	.	C	T	166.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;ClippingRankSum=0.141;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.66;MQRankSum=-1.065e+00;QD=3.70;ReadPosRankSum=1.32;SOR=0.638	GT:AD:DP:GQ:PL	0/1:33,12:45:99:174,0,710
+21	10028325	.	C	A	137.97	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.69;QD=23.00;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,6:6:18:152,18,0
+21	10029217	.	G	A	34.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=1.03;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.10;MQRankSum=1.03;QD=8.66;ReadPosRankSum=-1.026e+00;SOR=0.105	GT:AD:DP:GQ:PL	0/1:2,2:4:40:42,0,40
+21	10029407	.	A	G	124.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.230e-01;ClippingRankSum=-1.203e+00;DP=46;ExcessHet=3.0103;FS=21.891;MLEAC=1;MLEAF=0.500;MQ=37.52;MQRankSum=-4.780e-01;QD=2.71;ReadPosRankSum=-2.391e+00;SOR=4.405	GT:AD:DP:GQ:PL	0/1:38,8:46:99:132,0,1203
+21	10029437	.	A	G	84.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.147e+00;ClippingRankSum=-1.459e+00;DP=57;ExcessHet=3.0103;FS=13.341;MLEAC=1;MLEAF=0.500;MQ=36.58;MQRankSum=-3.560e-01;QD=1.48;ReadPosRankSum=0.310;SOR=3.386	GT:AD:DP:GQ:PL	0/1:49,8:57:92:92,0,1568
+21	10030170	.	C	G	58.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.600e-02;ClippingRankSum=-4.600e-02;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.37;MQRankSum=-1.871e+00;QD=2.55;ReadPosRankSum=1.05;SOR=0.036	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,3:23:66:0|1:10030170_C_G:66,0,980
+21	10030177	.	C	T	61.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.66;ClippingRankSum=0.151;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.53;MQRankSum=-1.759e+00;QD=2.94;ReadPosRankSum=0.352;SOR=0.043	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,3:21:69:0|1:10030170_C_G:69,0,945
+21	10031838	.	T	C	194.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.130e-01;ClippingRankSum=-8.720e-01;DP=21;ExcessHet=3.0103;FS=4.834;MLEAC=1;MLEAF=0.500;MQ=29.87;MQRankSum=2.06;QD=9.73;ReadPosRankSum=-2.694e+00;SOR=2.340	GT:AD:DP:GQ:PL	0/1:13,7:20:99:202,0,417
+21	10031861	.	C	A	95.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.18;ClippingRankSum=1.42;DP=32;ExcessHet=3.0103;FS=17.171;MLEAC=1;MLEAF=0.500;MQ=28.35;MQRankSum=1.52;QD=2.99;ReadPosRankSum=3.31;SOR=3.903	GT:AD:DP:GQ:PL	0/1:26,6:32:99:103,0,818
 21	10031912	.	TC	T	417.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.45;ClippingRankSum=-4.470e-01;DP=68;ExcessHet=3.0103;FS=6.596;MLEAC=1;MLEAF=0.500;MQ=26.92;MQRankSum=-9.780e-01;QD=6.14;ReadPosRankSum=1.98;SOR=1.802	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,14:68:99:0|1:10031912_TC_T:425,0,2251
-21	10031915	.	C	T	99.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.52;ClippingRankSum=-5.330e-01;DP=68;ExcessHet=3.0103;FS=2.909;MLEAC=1;MLEAF=0.500;MQ=26.92;MQRankSum=0.00;QD=1.46;ReadPosRankSum=2.45;SOR=1.218	GT:AD:DP:GQ:PL	0/1:57,11:68:99:107,0,2379
-21	10031923	.	C	A	429.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;ClippingRankSum=0.064;DP=58;ExcessHet=3.0103;FS=4.709;MLEAC=1;MLEAF=0.500;MQ=27.10;MQRankSum=-1.517e+00;QD=7.41;ReadPosRankSum=4.21;SOR=1.552	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,14:58:99:0|1:10031912_TC_T:437,0,2077
-21	10031942	.	T	C	475.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.985;ClippingRankSum=-9.180e-01;DP=49;ExcessHet=3.0103;FS=1.380;MLEAC=1;MLEAF=0.500;MQ=25.37;MQRankSum=0.719;QD=9.71;ReadPosRankSum=1.40;SOR=1.123	GT:AD:DP:GQ:PGT:PID:PL	0/1:35,14:49:99:0|1:10031912_TC_T:483,0,1393
-21	10032163	.	G	A	54.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.903;ClippingRankSum=-1.221e+00;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.58;MQRankSum=-5.840e-01;QD=3.03;ReadPosRankSum=-1.115e+00;SOR=1.329	GT:AD:DP:GQ:PL	0/1:14,4:18:62:62,0,412
-21	10032181	.	A	G	46.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.933;ClippingRankSum=0.284;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.93;MQRankSum=1.99;QD=2.03;ReadPosRankSum=2.39;SOR=0.245	GT:AD:DP:GQ:PL	0/1:19,4:23:54:54,0,531
-21	10032243	.	A	T	310.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.532e+00;ClippingRankSum=-5.420e-01;DP=29;ExcessHet=3.0103;FS=8.618;MLEAC=1;MLEAF=0.500;MQ=25.65;MQRankSum=0.966;QD=10.71;ReadPosRankSum=0.165;SOR=3.126	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,9:29:99:0|1:10032243_A_T:318,0,788
-21	10032248	.	C	T	310.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.28;ClippingRankSum=1.28;DP=28;ExcessHet=3.0103;FS=8.671;MLEAC=1;MLEAF=0.500;MQ=25.77;MQRankSum=0.935;QD=11.09;ReadPosRankSum=-4.900e-02;SOR=3.258	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,9:28:99:0|1:10032243_A_T:318,0,788
-21	10032274	.	A	G	397.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.100e+00;ClippingRankSum=-5.530e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.16;MQRankSum=0.092;QD=14.20;ReadPosRankSum=-1.380e-01;SOR=0.740	GT:AD:DP:GQ:PL	0/1:15,13:28:99:405,0,377
-21	10032275	.	G	A	102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;ClippingRankSum=-5.300e-02;DP=28;ExcessHet=3.0103;FS=22.368;MLEAC=1;MLEAF=0.500;MQ=26.16;MQRankSum=-3.180e-01;QD=3.66;ReadPosRankSum=0.106;SOR=4.163	GT:AD:DP:GQ:PL	0/1:21,7:28:99:110,0,768
+21	10031915	.	C	T	99.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.52;ClippingRankSum=-5.330e-01;DP=68;ExcessHet=3.0103;FS=2.909;MLEAC=1;MLEAF=0.500;MQ=26.92;MQRankSum=0.00;QD=1.47;ReadPosRankSum=2.45;SOR=1.218	GT:AD:DP:GQ:PL	0/1:57,11:68:99:107,0,2379
+21	10031923	.	C	A	429.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;ClippingRankSum=0.064;DP=58;ExcessHet=3.0103;FS=4.709;MLEAC=1;MLEAF=0.500;MQ=27.10;MQRankSum=-1.517e+00;QD=7.41;ReadPosRankSum=4.21;SOR=1.552	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,14:58:99:0|1:10031912_TC_T:437,0,2077
+21	10031942	.	T	C	475.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.985;ClippingRankSum=-9.180e-01;DP=49;ExcessHet=3.0103;FS=1.380;MLEAC=1;MLEAF=0.500;MQ=25.37;MQRankSum=0.719;QD=9.71;ReadPosRankSum=1.40;SOR=1.123	GT:AD:DP:GQ:PGT:PID:PL	0/1:35,14:49:99:0|1:10031912_TC_T:483,0,1393
+21	10032163	.	G	A	54.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.903;ClippingRankSum=-1.221e+00;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.58;MQRankSum=-5.840e-01;QD=3.04;ReadPosRankSum=-1.115e+00;SOR=1.329	GT:AD:DP:GQ:PL	0/1:14,4:18:62:62,0,412
+21	10032181	.	A	G	46.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.933;ClippingRankSum=0.284;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.93;MQRankSum=1.99;QD=2.03;ReadPosRankSum=2.39;SOR=0.245	GT:AD:DP:GQ:PL	0/1:19,4:23:54:54,0,531
+21	10032243	.	A	T	310.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.532e+00;ClippingRankSum=-5.420e-01;DP=29;ExcessHet=3.0103;FS=8.618;MLEAC=1;MLEAF=0.500;MQ=25.65;MQRankSum=0.966;QD=10.71;ReadPosRankSum=0.165;SOR=3.126	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,9:29:99:0|1:10032243_A_T:318,0,788
+21	10032248	.	C	T	310.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.28;ClippingRankSum=1.28;DP=28;ExcessHet=3.0103;FS=8.671;MLEAC=1;MLEAF=0.500;MQ=25.77;MQRankSum=0.935;QD=11.09;ReadPosRankSum=-4.900e-02;SOR=3.258	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,9:28:99:0|1:10032243_A_T:318,0,788
+21	10032274	.	A	G	397.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.100e+00;ClippingRankSum=-5.530e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.16;MQRankSum=0.092;QD=14.20;ReadPosRankSum=-1.380e-01;SOR=0.740	GT:AD:DP:GQ:PL	0/1:15,13:28:99:405,0,377
+21	10032275	.	G	A	102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;ClippingRankSum=-5.300e-02;DP=28;ExcessHet=3.0103;FS=22.368;MLEAC=1;MLEAF=0.500;MQ=26.16;MQRankSum=-3.180e-01;QD=3.67;ReadPosRankSum=0.106;SOR=4.163	GT:AD:DP:GQ:PL	0/1:21,7:28:99:110,0,768
 21	10032720	.	AT	A	49.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.79;MQRankSum=1.03;QD=12.40;ReadPosRankSum=0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:47:57,0,47
-21	10085023	.	G	A	504.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.06;ClippingRankSum=-5.160e-01;DP=263;ExcessHet=3.0103;FS=10.559;MLEAC=1;MLEAF=0.500;MQ=52.25;MQRankSum=1.32;QD=1.97;ReadPosRankSum=2.46;SOR=1.550	GT:AD:DP:GQ:PL	0/1:223,33:256:99:512,0,9136
-21	10085042	.	G	A	2451.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;ClippingRankSum=-6.310e-01;DP=250;ExcessHet=3.0103;FS=1.746;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=0.139;QD=10.30;ReadPosRankSum=0.386;SOR=0.837	GT:AD:DP:GQ:PL	0/1:165,73:238:99:2459,0,6631
+21	10085023	.	G	A	504.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.06;ClippingRankSum=-5.160e-01;DP=263;ExcessHet=3.0103;FS=10.559;MLEAC=1;MLEAF=0.500;MQ=52.25;MQRankSum=1.32;QD=1.97;ReadPosRankSum=2.46;SOR=1.550	GT:AD:DP:GQ:PL	0/1:223,33:256:99:512,0,9136
+21	10085042	.	G	A	2451.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;ClippingRankSum=-6.310e-01;DP=250;ExcessHet=3.0103;FS=1.746;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=0.139;QD=10.30;ReadPosRankSum=0.386;SOR=0.837	GT:AD:DP:GQ:PL	0/1:165,73:238:99:2459,0,6631
 21	10085060	.	GTGGAATGGAA	G	184.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.27;ClippingRankSum=-4.370e-01;DP=248;ExcessHet=3.0103;FS=16.069;MLEAC=1;MLEAF=0.500;MQ=48.63;MQRankSum=-3.490e+00;QD=0.98;ReadPosRankSum=-1.974e+00;SOR=2.424	GT:AD:DP:GQ:PL	0/1:171,18:189:99:192,0,7185
-21	10085097	.	T	G	400.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.533e+00;ClippingRankSum=0.344;DP=201;ExcessHet=3.0103;FS=1.731;MLEAC=1;MLEAF=0.500;MQ=46.77;MQRankSum=-5.170e-01;QD=3.28;ReadPosRankSum=-1.777e+00;SOR=0.929	GT:AD:DP:GQ:PL	0/1:100,22:131:99:408,0,5812
-21	10085102	.	G	T	515.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=-9.200e-01;DP=193;ExcessHet=3.0103;FS=4.069;MLEAC=1;MLEAF=0.500;MQ=46.34;MQRankSum=0.690;QD=2.93;ReadPosRankSum=0.264;SOR=0.374	GT:AD:DP:GQ:PL	0/1:148,28:176:99:523,0,5471
-21	10085128	.	G	T	103.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.030e-01;ClippingRankSum=-7.400e-02;DP=132;ExcessHet=3.0103;FS=8.815;MLEAC=1;MLEAF=0.500;MQ=44.76;MQRankSum=-1.453e+00;QD=0.89;ReadPosRankSum=-2.055e+00;SOR=1.997	GT:AD:DP:GQ:PL	0/1:104,13:117:99:111,0,4258
-21	10085135	.	T	TTGGAATGGAG	1165.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;ClippingRankSum=-4.020e-01;DP=121;ExcessHet=3.0103;FS=15.613;MLEAC=1;MLEAF=0.500;MQ=45.24;MQRankSum=-8.990e-01;QD=14.39;ReadPosRankSum=-2.701e+00;SOR=2.360	GT:AD:DP:GQ:PL	0/1:53,28:81:99:1173,0,2008
-21	10085152	.	A	G	750.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.152e+00;ClippingRankSum=-1.117e+00;DP=101;ExcessHet=3.0103;FS=17.835;MLEAC=1;MLEAF=0.500;MQ=47.28;MQRankSum=-1.821e+00;QD=7.99;ReadPosRankSum=-3.272e+00;SOR=2.972	GT:AD:DP:GQ:PL	0/1:71,23:94:99:758,0,2269
-21	10085222	.	G	T	506.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.900e-02;ClippingRankSum=-9.920e-01;DP=284;ExcessHet=3.0103;FS=10.342;MLEAC=1;MLEAF=0.500;MQ=45.79;MQRankSum=-6.990e-01;QD=1.79;ReadPosRankSum=-3.237e+00;SOR=1.126	GT:AD:DP:GQ:PL	0/1:242,41:283:99:514,0,8202
-21	10085345	.	A	AGAGTG	995.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;ClippingRankSum=0.732;DP=358;ExcessHet=3.0103;FS=1.297;MLEAC=1;MLEAF=0.500;MQ=55.20;MQRankSum=1.59;QD=3.67;ReadPosRankSum=-1.645e+00;SOR=0.555	GT:AD:DP:GQ:PL	0/1:227,44:271:99:1003,0,9002
-21	10085418	.	G	A	1743.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.06;ClippingRankSum=0.200;DP=202;ExcessHet=3.0103;FS=26.891;MLEAC=1;MLEAF=0.500;MQ=53.51;MQRankSum=-9.580e-01;QD=8.67;ReadPosRankSum=1.85;SOR=2.049	GT:AD:DP:GQ:PL	0/1:138,63:201:99:1751,0,4763
-21	10085473	.	G	A	135.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;ClippingRankSum=-8.950e-01;DP=198;ExcessHet=3.0103;FS=8.311;MLEAC=1;MLEAF=0.500;MQ=55.36;MQRankSum=3.68;QD=0.70;ReadPosRankSum=-2.203e+00;SOR=1.596	GT:AD:DP:GQ:PL	0/1:175,19:194:99:143,0,6064
-21	10085649	.	T	A	114.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.02;ClippingRankSum=0.805;DP=566;ExcessHet=3.0103;FS=2.282;MLEAC=1;MLEAF=0.500;MQ=51.57;MQRankSum=-7.588e+00;QD=0.20;ReadPosRankSum=5.29;SOR=0.449	GT:AD:DP:GQ:PL	0/1:524,40:564:99:122,0,21576
-21	10085669	.	A	G	60.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.743e+00;ClippingRankSum=0.338;DP=498;ExcessHet=3.0103;FS=11.041;MLEAC=1;MLEAF=0.500;MQ=51.10;MQRankSum=-5.543e+00;QD=0.12;ReadPosRankSum=3.09;SOR=2.143	GT:AD:DP:GQ:PL	0/1:462,36:498:68:68,0,19720
-21	10085695	.	G	GTGGAATGGAA	3465.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;ClippingRankSum=1.21;DP=447;ExcessHet=3.0103;FS=2.746;MLEAC=1;MLEAF=0.500;MQ=51.33;MQRankSum=-2.251e+00;QD=30.14;ReadPosRankSum=-2.362e+00;SOR=0.926	GT:AD:DP:GQ:PL	0/1:60,55:201:99:3473,0,2875
-21	10085892	.	A	G	19322.03	.	AC=2;AF=1.00;AN=2;DP=493;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.28;QD=25.36;SOR=1.332	GT:AD:DP:GQ:PL	1/1:0,492:492:99:19336,1486,0
-21	10085961	.	C	A	820.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=7.38;ClippingRankSum=-1.017e+00;DP=413;ExcessHet=3.0103;FS=12.931;MLEAC=1;MLEAF=0.500;MQ=45.73;MQRankSum=1.23;QD=2.00;ReadPosRankSum=1.51;SOR=1.887	GT:AD:DP:GQ:PL	0/1:356,55:411:99:828,0,10972
-21	10086156	.	A	ATGGAG	2549.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.210e-01;ClippingRankSum=-8.440e-01;DP=389;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.72;MQRankSum=-1.199e+00;QD=24.28;ReadPosRankSum=-2.918e+00;SOR=0.659	GT:AD:DP:GQ:PL	0/1:56,49:211:99:2557,0,2214
+21	10085097	.	T	G	400.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.533e+00;ClippingRankSum=0.344;DP=201;ExcessHet=3.0103;FS=1.731;MLEAC=1;MLEAF=0.500;MQ=46.77;MQRankSum=-5.170e-01;QD=3.28;ReadPosRankSum=-1.777e+00;SOR=0.929	GT:AD:DP:GQ:PL	0/1:100,22:131:99:408,0,5812
+21	10085102	.	G	T	515.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=-9.200e-01;DP=193;ExcessHet=3.0103;FS=4.069;MLEAC=1;MLEAF=0.500;MQ=46.34;MQRankSum=0.690;QD=2.93;ReadPosRankSum=0.264;SOR=0.374	GT:AD:DP:GQ:PL	0/1:148,28:176:99:523,0,5471
+21	10085128	.	G	T	103.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.030e-01;ClippingRankSum=-7.400e-02;DP=132;ExcessHet=3.0103;FS=8.815;MLEAC=1;MLEAF=0.500;MQ=44.76;MQRankSum=-1.453e+00;QD=0.89;ReadPosRankSum=-2.055e+00;SOR=1.997	GT:AD:DP:GQ:PL	0/1:104,13:117:99:111,0,4258
+21	10085135	.	T	TTGGAATGGAG	1165.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;ClippingRankSum=-4.020e-01;DP=121;ExcessHet=3.0103;FS=15.613;MLEAC=1;MLEAF=0.500;MQ=45.24;MQRankSum=-8.990e-01;QD=14.39;ReadPosRankSum=-2.701e+00;SOR=2.360	GT:AD:DP:GQ:PL	0/1:53,28:81:99:1173,0,2008
+21	10085152	.	A	G	750.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.152e+00;ClippingRankSum=-1.117e+00;DP=101;ExcessHet=3.0103;FS=17.835;MLEAC=1;MLEAF=0.500;MQ=47.28;MQRankSum=-1.821e+00;QD=7.99;ReadPosRankSum=-3.272e+00;SOR=2.972	GT:AD:DP:GQ:PL	0/1:71,23:94:99:758,0,2269
+21	10085222	.	G	T	506.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.900e-02;ClippingRankSum=-9.920e-01;DP=284;ExcessHet=3.0103;FS=10.342;MLEAC=1;MLEAF=0.500;MQ=45.79;MQRankSum=-6.990e-01;QD=1.79;ReadPosRankSum=-3.237e+00;SOR=1.126	GT:AD:DP:GQ:PL	0/1:242,41:283:99:514,0,8202
+21	10085345	.	A	AGAGTG	995.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;ClippingRankSum=0.732;DP=358;ExcessHet=3.0103;FS=1.297;MLEAC=1;MLEAF=0.500;MQ=55.20;MQRankSum=1.59;QD=3.67;ReadPosRankSum=-1.645e+00;SOR=0.555	GT:AD:DP:GQ:PL	0/1:227,44:271:99:1003,0,9002
+21	10085418	.	G	A	1743.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.06;ClippingRankSum=0.200;DP=202;ExcessHet=3.0103;FS=26.891;MLEAC=1;MLEAF=0.500;MQ=53.51;MQRankSum=-9.580e-01;QD=8.67;ReadPosRankSum=1.85;SOR=2.049	GT:AD:DP:GQ:PL	0/1:138,63:201:99:1751,0,4763
+21	10085473	.	G	A	135.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;ClippingRankSum=-8.950e-01;DP=198;ExcessHet=3.0103;FS=8.311;MLEAC=1;MLEAF=0.500;MQ=55.36;MQRankSum=3.68;QD=0.70;ReadPosRankSum=-2.203e+00;SOR=1.596	GT:AD:DP:GQ:PL	0/1:175,19:194:99:143,0,6064
+21	10085649	.	T	A	114.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.02;ClippingRankSum=0.805;DP=566;ExcessHet=3.0103;FS=2.282;MLEAC=1;MLEAF=0.500;MQ=51.57;MQRankSum=-7.588e+00;QD=0.20;ReadPosRankSum=5.29;SOR=0.449	GT:AD:DP:GQ:PL	0/1:524,40:564:99:122,0,21576
+21	10085669	.	A	G	60.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.743e+00;ClippingRankSum=0.338;DP=498;ExcessHet=3.0103;FS=11.041;MLEAC=1;MLEAF=0.500;MQ=51.10;MQRankSum=-5.543e+00;QD=0.12;ReadPosRankSum=3.09;SOR=2.143	GT:AD:DP:GQ:PL	0/1:462,36:498:68:68,0,19720
+21	10085695	.	G	GTGGAATGGAA	3465.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;ClippingRankSum=1.21;DP=447;ExcessHet=3.0103;FS=2.746;MLEAC=1;MLEAF=0.500;MQ=51.33;MQRankSum=-2.251e+00;QD=30.14;ReadPosRankSum=-2.362e+00;SOR=0.926	GT:AD:DP:GQ:PL	0/1:60,55:201:99:3473,0,2875
+21	10085892	.	A	G	19322.06	.	AC=2;AF=1.00;AN=2;DP=493;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.28;QD=25.36;SOR=1.332	GT:AD:DP:GQ:PL	1/1:0,492:492:99:19336,1486,0
+21	10085961	.	C	A	820.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=7.38;ClippingRankSum=-1.017e+00;DP=413;ExcessHet=3.0103;FS=12.931;MLEAC=1;MLEAF=0.500;MQ=45.73;MQRankSum=1.23;QD=2.00;ReadPosRankSum=1.51;SOR=1.887	GT:AD:DP:GQ:PL	0/1:356,55:411:99:828,0,10972
+21	10086156	.	A	ATGGAG	2549.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.210e-01;ClippingRankSum=-8.440e-01;DP=389;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.72;MQRankSum=-1.199e+00;QD=24.28;ReadPosRankSum=-2.918e+00;SOR=0.659	GT:AD:DP:GQ:PL	0/1:56,49:211:99:2557,0,2214
 21	10086216	.	ATGGAG	A	596.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.360e-01;ClippingRankSum=0.092;DP=435;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.88;MQRankSum=-1.039e+00;QD=2.54;ReadPosRankSum=0.530;SOR=0.721	GT:AD:DP:GQ:PL	0/1:203,32:266:99:604,0,9179
-21	10086286	.	G	GTGGAA	1519.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.65;ClippingRankSum=0.793;DP=424;ExcessHet=3.0103;FS=1.590;MLEAC=1;MLEAF=0.500;MQ=49.22;MQRankSum=-1.084e+00;QD=9.10;ReadPosRankSum=0.235;SOR=0.829	GT:AD:DP:GQ:PL	0/1:130,37:242:99:1527,0,5145
-21	10086299	.	G	GAATGC	1282.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.770e-01;ClippingRankSum=0.234;DP=407;ExcessHet=3.0103;FS=2.457;MLEAC=1;MLEAF=0.500;MQ=49.60;MQRankSum=-7.190e-01;QD=3.71;ReadPosRankSum=-1.262e+00;SOR=0.530	GT:AD:DP:GQ:PL	0/1:286,60:346:99:1290,0,10770
-21	10086366	.	G	GTGGAATGGAA	1926.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.468e+00;ClippingRankSum=0.149;DP=371;ExcessHet=3.0103;FS=67.741;MLEAC=1;MLEAF=0.500;MQ=46.15;MQRankSum=-1.763e+00;QD=7.50;ReadPosRankSum=-3.160e+00;SOR=3.928	GT:AD:DP:GQ:PL	0/1:198,59:257:99:1934,0,7728
-21	10086707	.	G	A	167.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.310;ClippingRankSum=-8.970e-01;DP=255;ExcessHet=3.0103;FS=11.623;MLEAC=1;MLEAF=0.500;MQ=37.79;MQRankSum=-2.387e+00;QD=0.66;ReadPosRankSum=-1.000e-03;SOR=1.888	GT:AD:DP:GQ:PL	0/1:232,23:255:99:175,0,9105
-21	10086709	.	T	TATGGA	1563.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.51;ClippingRankSum=-2.280e-01;DP=256;ExcessHet=3.0103;FS=23.234;MLEAC=1;MLEAF=0.500;MQ=38.03;MQRankSum=4.76;QD=10.42;ReadPosRankSum=1.51;SOR=0.084	GT:AD:DP:GQ:PL	0/1:127,23:156:99:1571,0,4950
-21	10086733	.	G	C	3201.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.454e+00;ClippingRankSum=1.63;DP=293;ExcessHet=3.0103;FS=134.429;MLEAC=1;MLEAF=0.500;MQ=39.68;MQRankSum=-9.546e+00;QD=14.42;ReadPosRankSum=0.602;SOR=4.321	GT:AD:DP:GQ:PL	0/1:145,77:249:99:3209,0,5183
-21	10086870	.	G	A	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.06;ClippingRankSum=-1.082e+00;DP=180;ExcessHet=3.0103;FS=11.195;MLEAC=1;MLEAF=0.500;MQ=28.93;MQRankSum=-2.329e+00;QD=0.55;ReadPosRankSum=0.862;SOR=2.956	GT:AD:DP:GQ:PGT:PID:PL	0/1:165,14:179:99:0|1:10086870_G_A:105,0,6605
-21	10086871	.	A	G	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276e+00;ClippingRankSum=-1.003e+00;DP=174;ExcessHet=3.0103;FS=11.170;MLEAC=1;MLEAF=0.500;MQ=28.49;MQRankSum=-2.547e+00;QD=0.56;ReadPosRankSum=0.284;SOR=2.891	GT:AD:DP:GQ:PGT:PID:PL	0/1:159,15:174:99:0|1:10086870_G_A:105,0,6605
-21	10086944	.	G	T	415.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;ClippingRankSum=0.110;DP=161;ExcessHet=3.0103;FS=1.859;MLEAC=1;MLEAF=0.500;MQ=35.63;MQRankSum=-1.453e+00;QD=2.60;ReadPosRankSum=0.294;SOR=0.946	GT:AD:DP:GQ:PL	0/1:132,28:160:99:423,0,4148
-21	10086950	.	G	T	50.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=0.727;DP=181;ExcessHet=3.0103;FS=10.024;MLEAC=1;MLEAF=0.500;MQ=37.06;MQRankSum=1.47;QD=0.28;ReadPosRankSum=0.785;SOR=0.359	GT:AD:DP:GQ:PL	0/1:164,17:181:58:58,0,5440
-21	10087037	.	G	GTGGAA	382.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.00;ClippingRankSum=0.552;DP=373;ExcessHet=3.0103;FS=20.690;MLEAC=1;MLEAF=0.500;MQ=44.60;MQRankSum=-4.411e+00;QD=1.71;ReadPosRankSum=-8.220e-01;SOR=1.962	GT:AD:DP:GQ:PL	0/1:201,23:249:99:390,0,8498
+21	10086286	.	G	GTGGAA	1519.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.65;ClippingRankSum=0.793;DP=424;ExcessHet=3.0103;FS=1.590;MLEAC=1;MLEAF=0.500;MQ=49.22;MQRankSum=-1.084e+00;QD=9.10;ReadPosRankSum=0.235;SOR=0.829	GT:AD:DP:GQ:PL	0/1:130,37:242:99:1527,0,5145
+21	10086299	.	G	GAATGC	1282.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.770e-01;ClippingRankSum=0.234;DP=407;ExcessHet=3.0103;FS=2.457;MLEAC=1;MLEAF=0.500;MQ=49.60;MQRankSum=-7.190e-01;QD=3.71;ReadPosRankSum=-1.262e+00;SOR=0.530	GT:AD:DP:GQ:PL	0/1:286,60:346:99:1290,0,10770
+21	10086366	.	G	GTGGAATGGAA	1926.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.468e+00;ClippingRankSum=0.149;DP=371;ExcessHet=3.0103;FS=67.741;MLEAC=1;MLEAF=0.500;MQ=46.15;MQRankSum=-1.763e+00;QD=7.50;ReadPosRankSum=-3.160e+00;SOR=3.928	GT:AD:DP:GQ:PL	0/1:198,59:257:99:1934,0,7728
+21	10086707	.	G	A	167.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.310;ClippingRankSum=-8.970e-01;DP=255;ExcessHet=3.0103;FS=11.623;MLEAC=1;MLEAF=0.500;MQ=37.79;MQRankSum=-2.387e+00;QD=0.66;ReadPosRankSum=-1.000e-03;SOR=1.888	GT:AD:DP:GQ:PL	0/1:232,23:255:99:175,0,9105
+21	10086709	.	T	TATGGA	1563.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.51;ClippingRankSum=-2.280e-01;DP=256;ExcessHet=3.0103;FS=23.234;MLEAC=1;MLEAF=0.500;MQ=38.03;MQRankSum=4.76;QD=10.42;ReadPosRankSum=1.51;SOR=0.084	GT:AD:DP:GQ:PL	0/1:127,23:156:99:1571,0,4950
+21	10086733	.	G	C	3201.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.454e+00;ClippingRankSum=1.63;DP=293;ExcessHet=3.0103;FS=134.429;MLEAC=1;MLEAF=0.500;MQ=39.68;MQRankSum=-9.546e+00;QD=14.42;ReadPosRankSum=0.602;SOR=4.321	GT:AD:DP:GQ:PL	0/1:145,77:249:99:3209,0,5183
+21	10086870	.	G	A	97.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.06;ClippingRankSum=-1.082e+00;DP=180;ExcessHet=3.0103;FS=11.195;MLEAC=1;MLEAF=0.500;MQ=28.93;MQRankSum=-2.329e+00;QD=0.55;ReadPosRankSum=0.862;SOR=2.956	GT:AD:DP:GQ:PGT:PID:PL	0/1:165,14:179:99:0|1:10086870_G_A:105,0,6605
+21	10086871	.	A	G	97.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276e+00;ClippingRankSum=-1.003e+00;DP=174;ExcessHet=3.0103;FS=11.170;MLEAC=1;MLEAF=0.500;MQ=28.49;MQRankSum=-2.547e+00;QD=0.56;ReadPosRankSum=0.284;SOR=2.891	GT:AD:DP:GQ:PGT:PID:PL	0/1:159,15:174:99:0|1:10086870_G_A:105,0,6605
+21	10086944	.	G	T	415.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;ClippingRankSum=0.110;DP=161;ExcessHet=3.0103;FS=1.859;MLEAC=1;MLEAF=0.500;MQ=35.63;MQRankSum=-1.453e+00;QD=2.60;ReadPosRankSum=0.294;SOR=0.946	GT:AD:DP:GQ:PL	0/1:132,28:160:99:423,0,4148
+21	10086950	.	G	T	50.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=0.727;DP=181;ExcessHet=3.0103;FS=10.024;MLEAC=1;MLEAF=0.500;MQ=37.06;MQRankSum=1.47;QD=0.28;ReadPosRankSum=0.785;SOR=0.359	GT:AD:DP:GQ:PL	0/1:164,17:181:58:58,0,5440
+21	10087037	.	G	GTGGAA	382.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.00;ClippingRankSum=0.552;DP=373;ExcessHet=3.0103;FS=20.690;MLEAC=1;MLEAF=0.500;MQ=44.60;MQRankSum=-4.411e+00;QD=1.71;ReadPosRankSum=-8.220e-01;SOR=1.962	GT:AD:DP:GQ:PL	0/1:201,23:249:99:390,0,8498
 21	10087062	.	AT	A	192.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=-8.260e-01;DP=362;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.12;MQRankSum=2.34;QD=0.71;ReadPosRankSum=3.48;SOR=0.615	GT:AD:DP:GQ:PGT:PID:PL	0/1:246,24:270:99:0|1:10087062_AT_A:200,0,9892
 21	10087063	.	TTGGAA	T	4419.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=-1.686e+00;DP=363;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.05;MQRankSum=1.01;QD=20.00;ReadPosRankSum=5.49;SOR=0.722	GT:AD:DP:GQ:PL	0/1:103,118:221:99:4427,0,3809
-21	10087068	.	A	AT	186.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.25;ClippingRankSum=-6.480e-01;DP=355;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.94;MQRankSum=2.36;QD=0.69;ReadPosRankSum=4.32;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:248,24:272:99:0|1:10087062_AT_A:194,0,9949
-21	10087127	.	G	C	89.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;ClippingRankSum=-1.000e-02;DP=182;ExcessHet=3.0103;FS=4.920;MLEAC=1;MLEAF=0.500;MQ=41.93;MQRankSum=0.411;QD=0.49;ReadPosRankSum=0.363;SOR=0.203	GT:AD:DP:GQ:PL	0/1:165,17:182:97:97,0,5582
-21	10087344	.	A	G	379.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.333e+00;ClippingRankSum=-1.000e-02;DP=159;ExcessHet=3.0103;FS=7.714;MLEAC=1;MLEAF=0.500;MQ=35.98;MQRankSum=-2.063e+00;QD=2.43;ReadPosRankSum=-6.800e-02;SOR=1.714	GT:AD:DP:GQ:PL	0/1:131,25:156:99:387,0,4953
-21	10087367	.	A	C	1283.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.061e+00;ClippingRankSum=-7.010e-01;DP=146;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.71;MQRankSum=-1.974e+00;QD=8.79;ReadPosRankSum=0.529;SOR=0.750	GT:AD:DP:GQ:PL	0/1:100,46:146:99:1291,0,3085
-21	10087395	.	G	GTGGAA	335.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.190e-01;ClippingRankSum=-9.710e-01;DP=123;ExcessHet=3.0103;FS=24.841;MLEAC=1;MLEAF=0.500;MQ=29.86;MQRankSum=0.432;QD=4.04;ReadPosRankSum=-7.580e-01;SOR=2.048	GT:AD:DP:GQ:PL	0/1:70,13:83:99:343,0,2776
-21	10087665	.	TGTGGAGTGGAGTGGA	T	554.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-02;ClippingRankSum=-3.490e-01;DP=66;ExcessHet=3.0103;FS=4.224;MLEAC=1;MLEAF=0.500;MQ=32.85;MQRankSum=0.371;QD=15.85;ReadPosRankSum=-2.780e+00;SOR=0.560	GT:AD:DP:GQ:PL	0/1:18,17:46:99:562,0,1004
-21	10087691	.	G	A	389.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.89;ClippingRankSum=-2.900e-02;DP=74;ExcessHet=3.0103;FS=4.167;MLEAC=1;MLEAF=0.500;MQ=31.83;MQRankSum=2.08;QD=5.57;ReadPosRankSum=2.78;SOR=1.419	GT:AD:DP:GQ:PL	0/1:55,15:70:99:397,0,2220
-21	10087696	.	G	A	626.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.85;ClippingRankSum=0.937;DP=85;ExcessHet=3.0103;FS=2.207;MLEAC=1;MLEAF=0.500;MQ=30.53;MQRankSum=1.62;QD=8.70;ReadPosRankSum=1.85;SOR=0.781	GT:AD:DP:GQ:PL	0/1:52,20:72:99:634,0,1939
-21	10087701	.	G	A	174.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.74;ClippingRankSum=0.369;DP=97;ExcessHet=3.0103;FS=8.844;MLEAC=1;MLEAF=0.500;MQ=29.71;MQRankSum=2.39;QD=2.33;ReadPosRankSum=1.83;SOR=1.787	GT:AD:DP:GQ:PL	0/1:67,8:75:99:182,0,2552
+21	10087068	.	A	AT	186.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.25;ClippingRankSum=-6.480e-01;DP=355;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.94;MQRankSum=2.36;QD=0.69;ReadPosRankSum=4.32;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:248,24:272:99:0|1:10087062_AT_A:194,0,9949
+21	10087127	.	G	C	89.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;ClippingRankSum=-1.000e-02;DP=182;ExcessHet=3.0103;FS=4.920;MLEAC=1;MLEAF=0.500;MQ=41.93;MQRankSum=0.411;QD=0.49;ReadPosRankSum=0.363;SOR=0.203	GT:AD:DP:GQ:PL	0/1:165,17:182:97:97,0,5582
+21	10087344	.	A	G	379.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.333e+00;ClippingRankSum=-1.000e-02;DP=159;ExcessHet=3.0103;FS=7.714;MLEAC=1;MLEAF=0.500;MQ=35.98;MQRankSum=-2.063e+00;QD=2.43;ReadPosRankSum=-6.800e-02;SOR=1.714	GT:AD:DP:GQ:PL	0/1:131,25:156:99:387,0,4953
+21	10087367	.	A	C	1283.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.061e+00;ClippingRankSum=-7.010e-01;DP=146;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.71;MQRankSum=-1.974e+00;QD=8.79;ReadPosRankSum=0.529;SOR=0.750	GT:AD:DP:GQ:PL	0/1:100,46:146:99:1291,0,3085
+21	10087395	.	G	GTGGAA	335.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.190e-01;ClippingRankSum=-9.710e-01;DP=123;ExcessHet=3.0103;FS=24.841;MLEAC=1;MLEAF=0.500;MQ=29.86;MQRankSum=0.432;QD=4.04;ReadPosRankSum=-7.580e-01;SOR=2.048	GT:AD:DP:GQ:PL	0/1:70,13:83:99:343,0,2776
+21	10087665	.	TGTGGAGTGGAGTGGA	T	554.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-02;ClippingRankSum=-3.490e-01;DP=66;ExcessHet=3.0103;FS=4.224;MLEAC=1;MLEAF=0.500;MQ=32.85;MQRankSum=0.371;QD=15.85;ReadPosRankSum=-2.780e+00;SOR=0.560	GT:AD:DP:GQ:PL	0/1:18,17:46:99:562,0,1004
+21	10087691	.	G	A	389.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.89;ClippingRankSum=-2.900e-02;DP=74;ExcessHet=3.0103;FS=4.167;MLEAC=1;MLEAF=0.500;MQ=31.83;MQRankSum=2.08;QD=5.57;ReadPosRankSum=2.78;SOR=1.419	GT:AD:DP:GQ:PL	0/1:55,15:70:99:397,0,2220
+21	10087696	.	G	A	626.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.85;ClippingRankSum=0.937;DP=85;ExcessHet=3.0103;FS=2.207;MLEAC=1;MLEAF=0.500;MQ=30.53;MQRankSum=1.62;QD=8.70;ReadPosRankSum=1.85;SOR=0.781	GT:AD:DP:GQ:PL	0/1:52,20:72:99:634,0,1939
+21	10087701	.	G	A	174.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.74;ClippingRankSum=0.369;DP=97;ExcessHet=3.0103;FS=8.844;MLEAC=1;MLEAF=0.500;MQ=29.71;MQRankSum=2.39;QD=2.33;ReadPosRankSum=1.83;SOR=1.787	GT:AD:DP:GQ:PL	0/1:67,8:75:99:182,0,2552
 21	10087873	.	CTGGAGTAGAGTGGAATGGAG	C	145.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.341;ClippingRankSum=-6.190e-01;DP=101;ExcessHet=3.0103;FS=1.615;MLEAC=1;MLEAF=0.500;MQ=32.87;MQRankSum=0.189;QD=2.65;ReadPosRankSum=1.23;SOR=1.131	GT:AD:DP:GQ:PL	0/1:48,7:55:99:153,0,1831
-21	10087950	.	A	G	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.104e+00;ClippingRankSum=0.255;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.76;MQRankSum=-8.500e-02;QD=2.51;ReadPosRankSum=1.27;SOR=0.045	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10087950_A_G:45,0,529
-21	10087953	.	A	G	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.613e+00;ClippingRankSum=-4.250e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.76;MQRankSum=0.425;QD=2.51;ReadPosRankSum=1.44;SOR=0.045	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10087950_A_G:45,0,529
-21	10087998	.	G	A	223.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.410e-01;ClippingRankSum=-6.050e-01;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.66;MQRankSum=-1.077e+00;QD=5.59;ReadPosRankSum=0.900;SOR=0.183	GT:AD:DP:GQ:PL	0/1:28,12:40:99:231,0,833
-21	10088045	.	G	T	134.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=-3.770e-01;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.89;MQRankSum=-1.745e+00;QD=2.32;ReadPosRankSum=-1.012e+00;SOR=0.061	GT:AD:DP:GQ:PL	0/1:47,11:58:99:142,0,1312
-21	10088202	.	A	G	118.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.710e-01;ClippingRankSum=0.373;DP=48;ExcessHet=3.0103;FS=10.577;MLEAC=1;MLEAF=0.500;MQ=28.01;MQRankSum=1.34;QD=2.47;ReadPosRankSum=2.42;SOR=3.056	GT:AD:DP:GQ:PL	0/1:40,8:48:99:126,0,1167
-21	10088339	.	A	T	55.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=27.64;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
-21	10088440	.	T	C	145.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.781e+00;ClippingRankSum=-1.044e+00;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.55;MQRankSum=-1.570e-01;QD=2.43;ReadPosRankSum=-3.853e+00;SOR=0.512	GT:AD:DP:GQ:PL	0/1:48,12:60:99:153,0,1350
-21	10088448	.	T	C	73.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.889e+00;ClippingRankSum=1.16;DP=81;ExcessHet=3.0103;FS=4.655;MLEAC=1;MLEAF=0.500;MQ=24.63;MQRankSum=-4.590e-01;QD=0.91;ReadPosRankSum=-2.838e+00;SOR=1.559	GT:AD:DP:GQ:PL	0/1:69,12:81:81:81,0,1965
-21	10088476	.	C	T	284.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.32;ClippingRankSum=-3.090e-01;DP=126;ExcessHet=3.0103;FS=3.061;MLEAC=1;MLEAF=0.500;MQ=27.35;MQRankSum=-1.850e+00;QD=2.26;ReadPosRankSum=2.27;SOR=0.577	GT:AD:DP:GQ:PL	0/1:103,23:126:99:292,0,2709
-21	10092871	.	T	G	1341.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.645;ClippingRankSum=1.19;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.94;MQRankSum=-1.732e+00;QD=26.29;ReadPosRankSum=0.510;SOR=2.428	GT:AD:DP:GQ:PL	1/1:1,50:51:99:1355,125,0
-21	10092931	.	T	G	272.02	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=24.73;SOR=1.802	GT:AD:DP:GQ:PL	1/1:0,11:11:33:286,33,0
-21	10098035	.	C	T	243.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.23;ClippingRankSum=-5.150e-01;DP=201;ExcessHet=3.0103;FS=18.555;MLEAC=1;MLEAF=0.500;MQ=20.04;MQRankSum=1.13;QD=1.22;ReadPosRankSum=3.86;SOR=2.500	GT:AD:DP:GQ:PL	0/1:173,27:200:99:251,0,3664
-21	10098377	.	T	C	31.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.250e-01;ClippingRankSum=-6.140e-01;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-3.310e-01;QD=1.58;ReadPosRankSum=-4.250e-01;SOR=0.083	GT:AD:DP:GQ:PL	0/1:16,4:20:39:39,0,321
-21	10101130	.	A	C	106.92	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=21.38;SOR=3.611	GT:AD:DP:GQ:PL	1/1:0,5:5:15:121,15,0
-21	10101225	.	A	AT	49.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=24.66;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
-21	10101300	.	A	G	323.02	.	AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=32.30;SOR=4.804	GT:AD:DP:GQ:PL	1/1:0,10:10:30:337,30,0
-21	10110730	.	G	A	103.10	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=25.77;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:117,12,0
-21	10110778	.	A	C	210.92	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=28.73;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10110778_A_C:225,15,0
-21	10110785	.	G	A	210.92	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=30.97;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10110778_A_C:225,15,0
-21	10110790	.	A	G	210.92	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=27.24;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10110778_A_C:225,15,0
-21	10110807	.	A	G	134.92	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=26.98;SOR=3.611	GT:AD:DP:GQ:PL	1/1:0,5:5:15:149,15,0
-21	10111039	.	T	C	105.10	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=26.27;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:119,12,0
-21	10112573	.	T	C	160.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.383e+00;ClippingRankSum=0.365;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.01;MQRankSum=-1.447e+00;QD=16.06;ReadPosRankSum=1.45;SOR=1.085	GT:AD:DP:GQ:PL	0/1:4,6:10:99:168,0,112
-21	10112597	.	G	A	192.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;ClippingRankSum=-1.179e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.27;MQRankSum=-6.700e-02;QD=21.40;ReadPosRankSum=1.18;SOR=2.093	GT:AD:DP:GQ:PL	0/1:2,7:9:47:200,0,47
-21	10112843	.	A	T	278.63	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.960e-01;ClippingRankSum=1.39;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.51;MQRankSum=-1.393e+00;QD=27.86;ReadPosRankSum=-6.960e-01;SOR=0.307	GT:AD:DP:GQ:PL	0/1:1,9:10:12:286,0,12
-21	10112869	.	T	A	295.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.00;ClippingRankSum=1.00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.06;MQRankSum=-2.310e-01;QD=22.74;ReadPosRankSum=1.62;SOR=0.307	GT:AD:DP:GQ:PL	0/1:4,9:13:99:303,0,115
-21	10113095	.	C	A	56.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.14;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-21	10113143	.	C	T	121.10	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=30.27;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:135,12,0
-21	10120154	.	T	G	36.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.594e+00;ClippingRankSum=-8.520e-01;DP=25;ExcessHet=3.0103;FS=12.478;MLEAC=1;MLEAF=0.500;MQ=32.20;MQRankSum=0.185;QD=1.46;ReadPosRankSum=-5.560e-01;SOR=0.009	GT:AD:DP:GQ:PL	0/1:21,4:25:44:44,0,624
+21	10087950	.	A	G	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.104e+00;ClippingRankSum=0.255;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.76;MQRankSum=-8.500e-02;QD=2.51;ReadPosRankSum=1.27;SOR=0.045	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10087950_A_G:45,0,529
+21	10087953	.	A	G	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.613e+00;ClippingRankSum=-4.250e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.76;MQRankSum=0.425;QD=2.51;ReadPosRankSum=1.44;SOR=0.045	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10087950_A_G:45,0,529
+21	10087998	.	G	A	223.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.410e-01;ClippingRankSum=-6.050e-01;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.66;MQRankSum=-1.077e+00;QD=5.59;ReadPosRankSum=0.900;SOR=0.183	GT:AD:DP:GQ:PL	0/1:28,12:40:99:231,0,833
+21	10088045	.	G	T	134.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=-3.770e-01;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.89;MQRankSum=-1.745e+00;QD=2.32;ReadPosRankSum=-1.012e+00;SOR=0.061	GT:AD:DP:GQ:PL	0/1:47,11:58:99:142,0,1312
+21	10088202	.	A	G	118.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.710e-01;ClippingRankSum=0.373;DP=48;ExcessHet=3.0103;FS=10.577;MLEAC=1;MLEAF=0.500;MQ=28.01;MQRankSum=1.34;QD=2.47;ReadPosRankSum=2.42;SOR=3.056	GT:AD:DP:GQ:PL	0/1:40,8:48:99:126,0,1167
+21	10088339	.	A	T	55.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=27.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:67,6,0
+21	10088440	.	T	C	145.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.781e+00;ClippingRankSum=-1.044e+00;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.55;MQRankSum=-1.570e-01;QD=2.43;ReadPosRankSum=-3.853e+00;SOR=0.512	GT:AD:DP:GQ:PL	0/1:48,12:60:99:153,0,1350
+21	10088448	.	T	C	73.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.889e+00;ClippingRankSum=1.16;DP=81;ExcessHet=3.0103;FS=4.655;MLEAC=1;MLEAF=0.500;MQ=24.63;MQRankSum=-4.590e-01;QD=0.91;ReadPosRankSum=-2.838e+00;SOR=1.559	GT:AD:DP:GQ:PL	0/1:69,12:81:81:81,0,1965
+21	10088476	.	C	T	284.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.32;ClippingRankSum=-3.090e-01;DP=126;ExcessHet=3.0103;FS=3.061;MLEAC=1;MLEAF=0.500;MQ=27.35;MQRankSum=-1.850e+00;QD=2.26;ReadPosRankSum=2.27;SOR=0.577	GT:AD:DP:GQ:PL	0/1:103,23:126:99:292,0,2709
+21	10092871	.	T	G	1341.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.645;ClippingRankSum=1.19;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.94;MQRankSum=-1.732e+00;QD=26.30;ReadPosRankSum=0.510;SOR=2.428	GT:AD:DP:GQ:PL	1/1:1,50:51:99:1355,125,0
+21	10092931	.	T	G	272.06	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=24.73;SOR=1.802	GT:AD:DP:GQ:PL	1/1:0,11:11:33:286,33,0
+21	10098035	.	C	T	243.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.23;ClippingRankSum=-5.150e-01;DP=201;ExcessHet=3.0103;FS=18.555;MLEAC=1;MLEAF=0.500;MQ=20.04;MQRankSum=1.13;QD=1.22;ReadPosRankSum=3.86;SOR=2.500	GT:AD:DP:GQ:PL	0/1:173,27:200:99:251,0,3664
+21	10098377	.	T	C	31.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.250e-01;ClippingRankSum=-6.140e-01;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-3.310e-01;QD=1.58;ReadPosRankSum=-4.250e-01;SOR=0.083	GT:AD:DP:GQ:PL	0/1:16,4:20:39:39,0,321
+21	10101130	.	A	C	106.96	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=21.39;SOR=3.611	GT:AD:DP:GQ:PL	1/1:0,5:5:15:121,15,0
+21	10101225	.	A	AT	49.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=24.64;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
+21	10101300	.	A	G	323.06	.	AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=32.31;SOR=4.804	GT:AD:DP:GQ:PL	1/1:0,10:10:30:337,30,0
+21	10110730	.	G	A	103.14	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=25.79;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:117,12,0
+21	10110778	.	A	C	210.96	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=28.73;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10110778_A_C:225,15,0
+21	10110785	.	G	A	210.96	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=30.97;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10110778_A_C:225,15,0
+21	10110790	.	A	G	210.96	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=27.24;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10110778_A_C:225,15,0
+21	10110807	.	A	G	134.96	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=26.99;SOR=3.611	GT:AD:DP:GQ:PL	1/1:0,5:5:15:149,15,0
+21	10111039	.	T	C	105.14	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=26.29;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:119,12,0
+21	10112573	.	T	C	160.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.383e+00;ClippingRankSum=0.365;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.01;MQRankSum=-1.447e+00;QD=16.06;ReadPosRankSum=1.45;SOR=1.085	GT:AD:DP:GQ:PL	0/1:4,6:10:99:168,0,112
+21	10112597	.	G	A	192.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;ClippingRankSum=-1.179e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.27;MQRankSum=-6.700e-02;QD=21.40;ReadPosRankSum=1.18;SOR=2.093	GT:AD:DP:GQ:PL	0/1:2,7:9:47:200,0,47
+21	10112843	.	A	T	278.67	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.960e-01;ClippingRankSum=1.39;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.51;MQRankSum=-1.393e+00;QD=27.87;ReadPosRankSum=-6.960e-01;SOR=0.307	GT:AD:DP:GQ:PL	0/1:1,9:10:12:286,0,12
+21	10112869	.	T	A	295.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.00;ClippingRankSum=1.00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.06;MQRankSum=-2.310e-01;QD=22.74;ReadPosRankSum=1.62;SOR=0.307	GT:AD:DP:GQ:PL	0/1:4,9:13:99:303,0,115
+21	10113095	.	C	A	56.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.16;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
+21	10113143	.	C	T	121.14	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=30.29;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:135,12,0
+21	10120154	.	T	G	36.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.594e+00;ClippingRankSum=-8.520e-01;DP=25;ExcessHet=3.0103;FS=12.478;MLEAC=1;MLEAF=0.500;MQ=32.20;MQRankSum=0.185;QD=1.47;ReadPosRankSum=-5.560e-01;SOR=0.009	GT:AD:DP:GQ:PL	0/1:21,4:25:44:44,0,624
 21	10120235	.	CACAGAG	C	296.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.892e+00;ClippingRankSum=-5.890e-01;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQRankSum=-1.519e+00;QD=16.48;ReadPosRankSum=0.713;SOR=0.425	GT:AD:DP:GQ:PL	0/1:13,5:23:99:304,0,510
 21	10120237	.	CAG	C	55.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.400e-01;ClippingRankSum=0.235;DP=39;ExcessHet=3.0103;FS=12.603;MLEAC=1;MLEAF=0.500;MQ=33.67;MQRankSum=0.783;QD=2.53;ReadPosRankSum=1.80;SOR=0.595	GT:AD:DP:GQ:PL	0/1:17,5:22:63:63,0,521
-21	10120436	.	T	G	81.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.77;MQRankSum=0.550;QD=11.66;ReadPosRankSum=0.937;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:89:89,0,97
-21	10120480	.	G	C	41.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;ClippingRankSum=0.957;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.78;MQRankSum=1.72;QD=1.89;ReadPosRankSum=-2.870e-01;SOR=0.039	GT:AD:DP:GQ:PL	0/1:19,3:22:49:49,0,585
-21	10120521	.	C	T	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=-7.400e-02;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.92;MQRankSum=0.149;QD=1.34;ReadPosRankSum=-2.230e-01;SOR=0.023	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,3:28:45:0|1:10120521_C_T:45,0,1125
-21	10120523	.	T	A	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.313e+00;ClippingRankSum=-2.770e-01;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQRankSum=0.968;QD=1.25;ReadPosRankSum=0.553;SOR=0.020	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:45:0|1:10120521_C_T:45,0,1125
-21	10120529	.	T	C	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.069;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQRankSum=0.138;QD=1.25;ReadPosRankSum=1.38;SOR=0.020	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:45:0|1:10120521_C_T:45,0,1125
-21	10120566	.	A	G	76.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.87;MQRankSum=1.53;QD=4.51;ReadPosRankSum=0.057;SOR=0.120	GT:AD:DP:GQ:PL	0/1:13,4:17:84:84,0,354
-21	10123484	.	G	C	121.80	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.20;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:10123484_G_C:135,9,0
-21	10123503	.	T	C	155.10	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=25.00;SOR=3.258	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,4:4:12:1|1:10123484_G_C:169,12,0
-21	10123552	.	C	A	143.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.200e-01;ClippingRankSum=-7.200e-01;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQRankSum=-7.200e-01;QD=23.93;ReadPosRankSum=-7.200e-01;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:72:0|1:10123552_C_A:151,0,72
-21	10123566	.	G	T	143.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=-3.580e-01;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQRankSum=1.23;QD=28.72;ReadPosRankSum=-3.580e-01;SOR=1.022	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,3:5:72:0|1:10123552_C_A:151,0,72
-21	10129029	.	T	A	38.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.03;MQRankSum=-1.026e+00;QD=9.65;ReadPosRankSum=1.03;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:46:46,0,53
-21	10129059	.	C	T	148.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.922;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.03;MQRankSum=0.00;QD=18.58;ReadPosRankSum=0.421;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,4:8:99:0|1:10129059_C_T:156,0,156
-21	10129069	.	A	G	145.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.610e-01;ClippingRankSum=0.361;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.14;MQRankSum=-3.610e-01;QD=16.18;ReadPosRankSum=0.361;SOR=0.527	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,4:9:99:0|1:10129059_C_T:153,0,187
-21	10129096	.	C	A	168.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.05;ClippingRankSum=1.10;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.39;MQRankSum=-2.363e+00;QD=10.54;ReadPosRankSum=-2.630e-01;SOR=0.693	GT:AD:DP:GQ:PL	0/1:8,8:16:99:176,0,245
-21	10129117	.	C	A	256.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=-9.560e-01;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.00;MQRankSum=-2.802e+00;QD=11.66;ReadPosRankSum=-1.650e-01;SOR=0.874	GT:AD:DP:GQ:PL	0/1:10,12:22:99:264,0,294
-21	10129125	.	A	C	852.03	.	AC=2;AF=1.00;AN=2;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.38;QD=29.56;SOR=6.273	GT:AD:DP:GQ:PL	1/1:0,22:22:66:866,66,0
-21	10129163	.	C	G	340.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.939;ClippingRankSum=-1.429e+00;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.40;MQRankSum=-3.144e+00;QD=17.93;ReadPosRankSum=-1.220e-01;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,9:19:99:0|1:10129163_C_G:348,0,393
-21	10129165	.	A	G	340.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.612;ClippingRankSum=-1.429e+00;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.40;MQRankSum=-3.633e+00;QD=17.93;ReadPosRankSum=-4.490e-01;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,9:19:99:0|1:10129163_C_G:348,0,393
-21	10129172	.	C	G	343.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.33;ClippingRankSum=0.530;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.25;MQRankSum=-3.179e+00;QD=19.09;ReadPosRankSum=-1.325e+00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:9,9:18:99:0|1:10129163_C_G:351,0,351
-21	10129184	.	A	T	127.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.194;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.81;MQRankSum=-2.905e+00;QD=9.11;ReadPosRankSum=-1.485e+00;SOR=0.473	GT:AD:DP:GQ:PL	0/1:8,6:14:99:135,0,231
-21	10129198	.	C	T	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;ClippingRankSum=0.466;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.94;MQRankSum=-1.749e+00;QD=8.87;ReadPosRankSum=-1.749e+00;SOR=0.551	GT:AD:DP:GQ:PL	0/1:6,5:11:99:105,0,177
-21	10129405	.	G	T	672.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.20;ClippingRankSum=2.40;DP=45;ExcessHet=3.0103;FS=2.549;MLEAC=1;MLEAF=0.500;MQ=33.19;MQRankSum=-3.105e+00;QD=14.95;ReadPosRankSum=1.54;SOR=0.993	GT:AD:DP:GQ:PL	0/1:21,24:45:99:680,0,607
-21	10129443	.	A	T	1090.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.000e-01;ClippingRankSum=0.720;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.42;MQRankSum=-3.358e+00;QD=13.98;ReadPosRankSum=1.05;SOR=0.693	GT:AD:DP:GQ:PL	0/1:39,39:78:99:1098,0,1319
-21	10129472	.	T	A	1079.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.38;ClippingRankSum=0.708;DP=50;ExcessHet=3.0103;FS=1.200;MLEAC=1;MLEAF=0.500;MQ=33.71;MQRankSum=-3.125e+00;QD=21.59;ReadPosRankSum=0.452;SOR=0.993	GT:AD:DP:GQ:PL	0/1:21,29:50:99:1087,0,507
-21	10129475	.	A	C	859.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249e+00;ClippingRankSum=-1.311e+00;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.80;MQRankSum=-1.546e+00;QD=18.29;ReadPosRankSum=1.05;SOR=0.671	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,25:47:99:0|1:10129475_A_C:867,0,1063
-21	10129484	.	C	G	699.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.916;ClippingRankSum=1.56;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.98;MQRankSum=-2.042e+00;QD=17.94;ReadPosRankSum=2.58;SOR=0.714	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,18:39:99:0|1:10129475_A_C:707,0,1004
-21	10129656	.	G	A	55.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;ClippingRankSum=1.18;DP=9;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=28.06;MQRankSum=1.67;QD=6.18;ReadPosRankSum=1.18;SOR=2.266	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,2:9:63:0|1:10129656_G_A:63,0,288
-21	10129665	.	T	G	49.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.118;ClippingRankSum=-1.180e-01;DP=11;ExcessHet=3.0103;FS=7.404;MLEAC=1;MLEAF=0.500;MQ=27.21;MQRankSum=2.00;QD=4.51;ReadPosRankSum=0.118;SOR=2.233	GT:AD:DP:GQ:PGT:PID:PL	0/1:9,2:11:57:0|1:10129656_G_A:57,0,337
+21	10120436	.	T	G	81.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.77;MQRankSum=0.550;QD=11.66;ReadPosRankSum=0.937;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:89:89,0,97
+21	10120480	.	G	C	41.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;ClippingRankSum=0.957;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.78;MQRankSum=1.72;QD=1.89;ReadPosRankSum=-2.870e-01;SOR=0.039	GT:AD:DP:GQ:PL	0/1:19,3:22:49:49,0,585
+21	10120521	.	C	T	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=-7.400e-02;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.92;MQRankSum=0.149;QD=1.34;ReadPosRankSum=-2.230e-01;SOR=0.023	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,3:28:45:0|1:10120521_C_T:45,0,1125
+21	10120523	.	T	A	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.313e+00;ClippingRankSum=-2.770e-01;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQRankSum=0.968;QD=1.25;ReadPosRankSum=0.553;SOR=0.020	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:45:0|1:10120521_C_T:45,0,1125
+21	10120529	.	T	C	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.069;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQRankSum=0.138;QD=1.25;ReadPosRankSum=1.38;SOR=0.020	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:45:0|1:10120521_C_T:45,0,1125
+21	10120566	.	A	G	76.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.87;MQRankSum=1.53;QD=4.51;ReadPosRankSum=0.057;SOR=0.120	GT:AD:DP:GQ:PL	0/1:13,4:17:84:84,0,354
+21	10123484	.	G	C	121.84	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.20;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:10123484_G_C:135,9,0
+21	10123503	.	T	C	155.14	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=25.00;SOR=3.258	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,4:4:12:1|1:10123484_G_C:169,12,0
+21	10123552	.	C	A	143.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.200e-01;ClippingRankSum=-7.200e-01;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQRankSum=-7.200e-01;QD=23.94;ReadPosRankSum=-7.200e-01;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:72:0|1:10123552_C_A:151,0,72
+21	10123566	.	G	T	143.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=-3.580e-01;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQRankSum=1.23;QD=28.73;ReadPosRankSum=-3.580e-01;SOR=1.022	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,3:5:72:0|1:10123552_C_A:151,0,72
+21	10129029	.	T	A	38.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.03;MQRankSum=-1.026e+00;QD=9.66;ReadPosRankSum=1.03;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:46:46,0,53
+21	10129059	.	C	T	148.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.922;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.03;MQRankSum=0.00;QD=18.58;ReadPosRankSum=0.421;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,4:8:99:0|1:10129059_C_T:156,0,156
+21	10129069	.	A	G	145.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.610e-01;ClippingRankSum=0.361;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.14;MQRankSum=-3.610e-01;QD=16.18;ReadPosRankSum=0.361;SOR=0.527	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,4:9:99:0|1:10129059_C_T:153,0,187
+21	10129096	.	C	A	168.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.05;ClippingRankSum=1.10;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.39;MQRankSum=-2.363e+00;QD=10.54;ReadPosRankSum=-2.630e-01;SOR=0.693	GT:AD:DP:GQ:PL	0/1:8,8:16:99:176,0,245
+21	10129117	.	C	A	256.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=-9.560e-01;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.00;MQRankSum=-2.802e+00;QD=11.67;ReadPosRankSum=-1.650e-01;SOR=0.874	GT:AD:DP:GQ:PL	0/1:10,12:22:99:264,0,294
+21	10129125	.	A	C	852.06	.	AC=2;AF=1.00;AN=2;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.38;QD=29.56;SOR=6.273	GT:AD:DP:GQ:PL	1/1:0,22:22:66:866,66,0
+21	10129163	.	C	G	340.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.939;ClippingRankSum=-1.429e+00;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.40;MQRankSum=-3.144e+00;QD=17.93;ReadPosRankSum=-1.220e-01;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,9:19:99:0|1:10129163_C_G:348,0,393
+21	10129165	.	A	G	340.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.612;ClippingRankSum=-1.429e+00;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.40;MQRankSum=-3.633e+00;QD=17.93;ReadPosRankSum=-4.490e-01;SOR=0.602	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,9:19:99:0|1:10129163_C_G:348,0,393
+21	10129172	.	C	G	343.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.33;ClippingRankSum=0.530;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.25;MQRankSum=-3.179e+00;QD=19.09;ReadPosRankSum=-1.325e+00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:9,9:18:99:0|1:10129163_C_G:351,0,351
+21	10129184	.	A	T	127.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.194;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.81;MQRankSum=-2.905e+00;QD=9.12;ReadPosRankSum=-1.485e+00;SOR=0.473	GT:AD:DP:GQ:PL	0/1:8,6:14:99:135,0,231
+21	10129198	.	C	T	97.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;ClippingRankSum=0.466;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.94;MQRankSum=-1.749e+00;QD=8.88;ReadPosRankSum=-1.749e+00;SOR=0.551	GT:AD:DP:GQ:PL	0/1:6,5:11:99:105,0,177
+21	10129405	.	G	T	672.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.20;ClippingRankSum=2.40;DP=45;ExcessHet=3.0103;FS=2.549;MLEAC=1;MLEAF=0.500;MQ=33.19;MQRankSum=-3.105e+00;QD=14.95;ReadPosRankSum=1.54;SOR=0.993	GT:AD:DP:GQ:PL	0/1:21,24:45:99:680,0,607
+21	10129443	.	A	T	1090.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.000e-01;ClippingRankSum=0.720;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.42;MQRankSum=-3.358e+00;QD=13.98;ReadPosRankSum=1.05;SOR=0.693	GT:AD:DP:GQ:PL	0/1:39,39:78:99:1098,0,1319
+21	10129472	.	T	A	1079.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.38;ClippingRankSum=0.708;DP=50;ExcessHet=3.0103;FS=1.200;MLEAC=1;MLEAF=0.500;MQ=33.71;MQRankSum=-3.125e+00;QD=21.59;ReadPosRankSum=0.452;SOR=0.993	GT:AD:DP:GQ:PL	0/1:21,29:50:99:1087,0,507
+21	10129475	.	A	C	859.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249e+00;ClippingRankSum=-1.311e+00;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.80;MQRankSum=-1.546e+00;QD=18.29;ReadPosRankSum=1.05;SOR=0.671	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,25:47:99:0|1:10129475_A_C:867,0,1063
+21	10129484	.	C	G	699.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.916;ClippingRankSum=1.56;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.98;MQRankSum=-2.042e+00;QD=17.94;ReadPosRankSum=2.58;SOR=0.714	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,18:39:99:0|1:10129475_A_C:707,0,1004
+21	10129656	.	G	A	55.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;ClippingRankSum=1.18;DP=9;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=28.06;MQRankSum=1.67;QD=6.18;ReadPosRankSum=1.18;SOR=2.266	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,2:9:63:0|1:10129656_G_A:63,0,288
+21	10129665	.	T	G	49.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.118;ClippingRankSum=-1.180e-01;DP=11;ExcessHet=3.0103;FS=7.404;MLEAC=1;MLEAF=0.500;MQ=27.21;MQRankSum=2.00;QD=4.51;ReadPosRankSum=0.118;SOR=2.233	GT:AD:DP:GQ:PGT:PID:PL	0/1:9,2:11:57:0|1:10129656_G_A:57,0,337
 21	10129697	.	GAA	G	270.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.202e+00;ClippingRankSum=-3.340e-01;DP=23;ExcessHet=3.0103;FS=22.583;MLEAC=1;MLEAF=0.500;MQ=27.67;MQRankSum=1.34;QD=12.30;ReadPosRankSum=-1.002e+00;SOR=4.610	GT:AD:DP:GQ:PL	0/1:13,9:22:99:278,0,397
-21	10129737	.	T	C	604.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.804e+00;ClippingRankSum=-8.320e-01;DP=34;ExcessHet=3.0103;FS=23.451;MLEAC=1;MLEAF=0.500;MQ=28.35;MQRankSum=2.29;QD=17.78;ReadPosRankSum=1.08;SOR=4.977	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,15:34:99:0|1:10129737_T_C:612,0,757
-21	10129749	.	T	A	727.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.149e+00;ClippingRankSum=0.323;DP=40;ExcessHet=3.0103;FS=16.947;MLEAC=1;MLEAF=0.500;MQ=28.45;MQRankSum=-1.830e-01;QD=18.66;ReadPosRankSum=-7.160e-01;SOR=4.479	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,19:39:99:0|1:10129737_T_C:735,0,811
-21	10129766	.	G	A	745.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;ClippingRankSum=-4.190e-01;DP=41;ExcessHet=3.0103;FS=9.746;MLEAC=1;MLEAF=0.500;MQ=28.83;MQRankSum=-9.060e-01;QD=18.64;ReadPosRankSum=-1.474e+00;SOR=3.667	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,20:40:99:0|1:10129737_T_C:753,0,744
-21	10129836	.	G	A	31.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=-5.560e-01;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.76;MQRankSum=-2.302e+00;QD=1.98;ReadPosRankSum=0.079;SOR=0.169	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,2:16:39:0|1:10129826_G_T:39,0,620
-21	10129856	.	G	T	64.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.720;DP=6;ExcessHet=3.0103;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=30.12;MQRankSum=-7.200e-01;QD=10.77;ReadPosRankSum=0.720;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,2:6:72:0|1:10129856_G_T:72,0,130
-21	10129863	.	C	A	70.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=32.42;MQRankSum=-1.026e+00;QD=17.65;ReadPosRankSum=-1.026e+00;SOR=2.209	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,2:4:78:0|1:10129856_G_T:78,0,78
-21	10130081	.	A	G	55.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;ClippingRankSum=-2.890e-01;DP=12;ExcessHet=3.0103;FS=12.175;MLEAC=1;MLEAF=0.500;MQ=24.04;MQRankSum=-2.637e+00;QD=4.63;ReadPosRankSum=2.18;SOR=3.226	GT:AD:DP:GQ:PL	0/1:8,4:12:63:63,0,201
-21	10130104	.	T	C	73.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.720;DP=6;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=22.25;MQRankSum=-1.380e+00;QD=12.27;ReadPosRankSum=-1.380e+00;SOR=3.258	GT:AD:DP:GQ:PL	0/1:2,4:6:41:81,0,41
-21	10130924	.	A	T	141.10	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.00;QD=30.62;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:155,12,0
+21	10129737	.	T	C	604.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.804e+00;ClippingRankSum=-8.320e-01;DP=34;ExcessHet=3.0103;FS=23.451;MLEAC=1;MLEAF=0.500;MQ=28.35;MQRankSum=2.29;QD=17.78;ReadPosRankSum=1.08;SOR=4.977	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,15:34:99:0|1:10129737_T_C:612,0,757
+21	10129749	.	T	A	727.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.149e+00;ClippingRankSum=0.323;DP=40;ExcessHet=3.0103;FS=16.947;MLEAC=1;MLEAF=0.500;MQ=28.45;MQRankSum=-1.830e-01;QD=18.66;ReadPosRankSum=-7.160e-01;SOR=4.479	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,19:39:99:0|1:10129737_T_C:735,0,811
+21	10129766	.	G	A	745.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;ClippingRankSum=-4.190e-01;DP=41;ExcessHet=3.0103;FS=9.746;MLEAC=1;MLEAF=0.500;MQ=28.83;MQRankSum=-9.060e-01;QD=18.64;ReadPosRankSum=-1.474e+00;SOR=3.667	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,20:40:99:0|1:10129737_T_C:753,0,744
+21	10129836	.	G	A	31.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=-5.560e-01;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.76;MQRankSum=-2.302e+00;QD=1.98;ReadPosRankSum=0.079;SOR=0.169	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,2:16:39:0|1:10129826_G_T:39,0,620
+21	10129856	.	G	T	64.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.720;DP=6;ExcessHet=3.0103;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=30.12;MQRankSum=-7.200e-01;QD=10.77;ReadPosRankSum=0.720;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,2:6:72:0|1:10129856_G_T:72,0,130
+21	10129863	.	C	A	70.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=32.42;MQRankSum=-1.026e+00;QD=17.66;ReadPosRankSum=-1.026e+00;SOR=2.209	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,2:4:78:0|1:10129856_G_T:78,0,78
+21	10130081	.	A	G	55.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;ClippingRankSum=-2.890e-01;DP=12;ExcessHet=3.0103;FS=12.175;MLEAC=1;MLEAF=0.500;MQ=24.04;MQRankSum=-2.637e+00;QD=4.64;ReadPosRankSum=2.18;SOR=3.226	GT:AD:DP:GQ:PL	0/1:8,4:12:63:63,0,201
+21	10130104	.	T	C	73.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.720;DP=6;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=22.25;MQRankSum=-1.380e+00;QD=12.27;ReadPosRankSum=-1.380e+00;SOR=3.258	GT:AD:DP:GQ:PL	0/1:2,4:6:41:81,0,41
+21	10130924	.	A	T	141.14	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.00;QD=30.62;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:155,12,0
 21	10130987	.	CAT	C	208.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.92;ClippingRankSum=0.702;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.66;MQRankSum=-1.733e+00;QD=11.59;ReadPosRankSum=0.515;SOR=0.223	GT:AD:DP:GQ:PL	0/1:12,6:18:99:216,0,477
-21	10131001	.	G	A	207.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.91;ClippingRankSum=-5.210e-01;DP=15;ExcessHet=3.0103;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=32.38;MQRankSum=0.521;QD=13.84;ReadPosRankSum=-7.520e-01;SOR=2.546	GT:AD:DP:GQ:PL	0/1:8,7:15:99:215,0,227
-21	10131216	.	A	G	125.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.286e+00;ClippingRankSum=-3.060e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.43;MQRankSum=-2.633e+00;QD=8.37;ReadPosRankSum=-6.740e-01;SOR=0.260	GT:AD:DP:GQ:PL	0/1:10,5:15:99:133,0,325
-21	10131234	.	G	C	56.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=-1.090e+00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.39;MQRankSum=-2.335e+00;QD=4.04;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PL	0/1:11,3:14:64:64,0,371
-21	10131915	.	A	G	63.80	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=21.27;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:77,9,0
-21	10132196	.	G	A	152.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.01;ClippingRankSum=0.412;DP=15;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=37.46;MQRankSum=-8.840e-01;QD=10.17;ReadPosRankSum=-5.900e-02;SOR=1.981	GT:AD:DP:GQ:PL	0/1:9,6:15:99:160,0,298
-21	10132241	.	T	C	58.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.516e+00;ClippingRankSum=-2.170e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.46;MQRankSum=0.361;QD=3.91;ReadPosRankSum=0.361;SOR=0.527	GT:AD:DP:GQ:PL	0/1:12,3:15:66:66,0,358
-21	10132511	.	C	T	32.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.50;ClippingRankSum=-9.220e-01;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.42;MQRankSum=-9.220e-01;QD=4.66;ReadPosRankSum=-1.980e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/1:5,2:7:40:40,0,142
+21	10131001	.	G	A	207.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.91;ClippingRankSum=-5.210e-01;DP=15;ExcessHet=3.0103;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=32.38;MQRankSum=0.521;QD=13.84;ReadPosRankSum=-7.520e-01;SOR=2.546	GT:AD:DP:GQ:PL	0/1:8,7:15:99:215,0,227
+21	10131216	.	A	G	125.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.286e+00;ClippingRankSum=-3.060e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.43;MQRankSum=-2.633e+00;QD=8.38;ReadPosRankSum=-6.740e-01;SOR=0.260	GT:AD:DP:GQ:PL	0/1:10,5:15:99:133,0,325
+21	10131234	.	G	C	56.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=-1.090e+00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.39;MQRankSum=-2.335e+00;QD=4.05;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PL	0/1:11,3:14:64:64,0,371
+21	10131915	.	A	G	63.84	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=21.28;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:77,9,0
+21	10132196	.	G	A	152.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.01;ClippingRankSum=0.412;DP=15;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=37.46;MQRankSum=-8.840e-01;QD=10.18;ReadPosRankSum=-5.900e-02;SOR=1.981	GT:AD:DP:GQ:PL	0/1:9,6:15:99:160,0,298
+21	10132241	.	T	C	58.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.516e+00;ClippingRankSum=-2.170e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.46;MQRankSum=0.361;QD=3.91;ReadPosRankSum=0.361;SOR=0.527	GT:AD:DP:GQ:PL	0/1:12,3:15:66:66,0,358
+21	10132511	.	C	T	32.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.50;ClippingRankSum=-9.220e-01;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.42;MQRankSum=-9.220e-01;QD=4.66;ReadPosRankSum=-1.980e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/1:5,2:7:40:40,0,142
 21	10135244	.	TCAGAGGTCCCCACCTAA	T	193.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920e+00;ClippingRankSum=0.956;DP=9;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=29.50;MQRankSum=1.92;QD=24.20;ReadPosRankSum=-1.920e+00;SOR=2.833	GT:AD:DP:GQ:PL	0/1:3,5:8:99:201,0,111
-21	10135272	.	T	C	96.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.74;MQRankSum=1.54;QD=16.10;SOR=2.093	GT:AD:DP:GQ:PL	0/1:3,3:6:99:104,0,117
-21	10135511	.	A	G	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.580e-01;ClippingRankSum=-1.231e+00;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQRankSum=1.23;QD=18.52;ReadPosRankSum=-3.580e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:48:100,0,48
-21	10135540	.	C	T	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQRankSum=1.23;QD=18.52;ReadPosRankSum=0.358;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:48:100,0,48
-21	10136335	.	A	G	102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=-1.281e+00;DP=18;ExcessHet=3.0103;FS=14.443;MLEAC=1;MLEAF=0.500;MQ=30.69;MQRankSum=-1.873e+00;QD=5.70;ReadPosRankSum=0.690;SOR=3.596	GT:AD:DP:GQ:PL	0/1:13,5:18:99:110,0,376
-21	10136414	.	C	G	1220.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.79;ClippingRankSum=-5.640e-01;DP=125;ExcessHet=3.0103;FS=12.383;MLEAC=1;MLEAF=0.500;MQ=30.73;MQRankSum=-3.834e+00;QD=9.84;ReadPosRankSum=-5.200e-02;SOR=3.109	GT:AD:DP:GQ:PGT:PID:PL	0/1:88,36:124:99:0|1:10136414_C_G:1228,0,3595
-21	10136415	.	A	G	1220.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176e+00;ClippingRankSum=0.300;DP=125;ExcessHet=3.0103;FS=12.233;MLEAC=1;MLEAF=0.500;MQ=30.82;MQRankSum=-3.348e+00;QD=9.84;ReadPosRankSum=0.788;SOR=3.033	GT:AD:DP:GQ:PGT:PID:PL	0/1:89,35:124:99:0|1:10136414_C_G:1228,0,3595
-21	10136435	.	A	C	1409.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.974e+00;ClippingRankSum=1.01;DP=137;ExcessHet=3.0103;FS=9.748;MLEAC=1;MLEAF=0.500;MQ=30.67;MQRankSum=-4.618e+00;QD=10.29;ReadPosRankSum=0.215;SOR=2.638	GT:AD:DP:GQ:PGT:PID:PL	0/1:97,40:137:99:0|1:10136435_A_C:1417,0,3950
-21	10136440	.	C	T	1406.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.09;ClippingRankSum=1.38;DP=139;ExcessHet=3.0103;FS=9.801;MLEAC=1;MLEAF=0.500;MQ=30.65;MQRankSum=-3.614e+00;QD=10.12;ReadPosRankSum=0.164;SOR=2.663	GT:AD:DP:GQ:PGT:PID:PL	0/1:98,41:139:99:0|1:10136435_A_C:1414,0,3980
-21	10136444	.	A	T	260.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.712e+00;ClippingRankSum=0.269;DP=141;ExcessHet=3.0103;FS=2.265;MLEAC=1;MLEAF=0.500;MQ=30.57;MQRankSum=0.752;QD=1.85;ReadPosRankSum=0.601;SOR=1.066	GT:AD:DP:GQ:PL	0/1:122,19:141:99:268,0,4274
-21	10136495	.	G	T	690.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=0.773;DP=93;ExcessHet=3.0103;FS=4.818;MLEAC=1;MLEAF=0.500;MQ=31.61;MQRankSum=-2.310e-01;QD=7.43;ReadPosRankSum=-6.550e-01;SOR=1.939	GT:AD:DP:GQ:PGT:PID:PL	0/1:71,22:93:99:0|1:10136495_G_T:698,0,2892
-21	10136496	.	C	A	690.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.21;ClippingRankSum=-1.364e+00;DP=90;ExcessHet=3.0103;FS=4.823;MLEAC=1;MLEAF=0.500;MQ=31.69;MQRankSum=-9.060e-01;QD=7.67;ReadPosRankSum=-6.200e-01;SOR=1.915	GT:AD:DP:GQ:PGT:PID:PL	0/1:69,21:90:99:0|1:10136495_G_T:698,0,2892
-21	10136523	.	C	G	206.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;ClippingRankSum=-1.660e-01;DP=63;ExcessHet=3.0103;FS=9.814;MLEAC=1;MLEAF=0.500;MQ=32.90;MQRankSum=-1.794e+00;QD=3.28;ReadPosRankSum=-1.969e+00;SOR=2.739	GT:AD:DP:GQ:PL	0/1:51,12:63:99:214,0,1606
-21	10136538	.	A	G	32.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.435;DP=53;ExcessHet=3.0103;FS=4.987;MLEAC=1;MLEAF=0.500;MQ=33.17;MQRankSum=-1.333e+00;QD=0.62;ReadPosRankSum=-2.625e+00;SOR=2.000	GT:AD:DP:GQ:PL	0/1:47,6:53:40:40,0,1604
-21	10136562	.	T	G	302.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;ClippingRankSum=0.230;DP=43;ExcessHet=3.0103;FS=25.046;MLEAC=1;MLEAF=0.500;MQ=31.44;MQRankSum=1.12;QD=7.04;ReadPosRankSum=-2.030e-01;SOR=5.015	GT:AD:DP:GQ:PL	0/1:31,12:43:99:310,0,854
-21	10136666	.	T	A	272.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.47;ClippingRankSum=-1.267e+00;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.95;MQRankSum=2.43;QD=5.05;ReadPosRankSum=-2.100e-02;SOR=0.495	GT:AD:DP:GQ:PL	0/1:43,11:54:99:280,0,1602
-21	10136694	.	A	G	697.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.602e+00;ClippingRankSum=-6.990e-01;DP=170;ExcessHet=3.0103;FS=63.316;MLEAC=1;MLEAF=0.500;MQ=36.33;MQRankSum=-6.964e+00;QD=4.10;ReadPosRankSum=-3.300e-02;SOR=4.804	GT:AD:DP:GQ:PL	0/1:136,34:170:99:705,0,4769
-21	10136744	.	ATTT	A	707.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.45;ClippingRankSum=-2.387e+00;DP=368;ExcessHet=3.0103;FS=235.351;MLEAC=1;MLEAF=0.500;MQ=36.63;MQRankSum=-9.813e+00;QD=2.15;ReadPosRankSum=-1.963e+00;SOR=8.468	GT:AD:DP:GQ:PL	0/1:296,33:364:99:715,0,12396
-21	10136757	.	G	A	4213.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;ClippingRankSum=0.140;DP=368;ExcessHet=3.0103;FS=20.497;MLEAC=1;MLEAF=0.500;MQ=36.51;MQRankSum=-1.422e+01;QD=11.48;ReadPosRankSum=1.84;SOR=1.183	GT:AD:DP:GQ:PL	0/1:235,132:367:99:4221,0,7848
-21	10136761	.	C	T	1890.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.99;ClippingRankSum=9.000e-03;DP=350;ExcessHet=3.0103;FS=209.122;MLEAC=1;MLEAF=0.500;MQ=36.50;MQRankSum=-1.010e+01;QD=5.40;ReadPosRankSum=2.10;SOR=8.468	GT:AD:DP:GQ:PL	0/1:282,68:350:99:1898,0,11595
-21	10136776	.	T	C	2065.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.609e+00;ClippingRankSum=0.255;DP=290;ExcessHet=3.0103;FS=212.054;MLEAC=1;MLEAF=0.500;MQ=36.20;MQRankSum=-9.326e+00;QD=7.12;ReadPosRankSum=0.885;SOR=8.739	GT:AD:DP:GQ:PL	0/1:212,78:290:99:2073,0,7770
-21	10136796	.	G	A	298.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.954;ClippingRankSum=-1.300e+00;DP=228;ExcessHet=3.0103;FS=61.643;MLEAC=1;MLEAF=0.500;MQ=35.70;MQRankSum=-4.788e+00;QD=1.31;ReadPosRankSum=-2.310e+00;SOR=2.881	GT:AD:DP:GQ:PGT:PID:PL	0/1:204,24:228:99:0|1:10136796_G_A:306,0,8349
-21	10136804	.	T	G	181.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.604e+00;ClippingRankSum=0.203;DP=201;ExcessHet=3.0103;FS=39.016;MLEAC=1;MLEAF=0.500;MQ=35.61;MQRankSum=-4.861e+00;QD=0.90;ReadPosRankSum=-1.905e+00;SOR=2.079	GT:AD:DP:GQ:PGT:PID:PL	0/1:184,17:201:99:0|1:10136796_G_A:189,0,7868
-21	10136892	.	G	C	677.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.308e+00;ClippingRankSum=-5.400e-02;DP=33;ExcessHet=3.0103;FS=18.978;MLEAC=1;MLEAF=0.500;MQ=26.42;MQRankSum=-1.320e+00;QD=20.53;ReadPosRankSum=0.777;SOR=4.686	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,18:33:99:0|1:10136885_G_T:685,0,841
-21	10136897	.	A	G	556.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.030e-01;ClippingRankSum=-2.470e-01;DP=32;ExcessHet=3.0103;FS=16.234;MLEAC=1;MLEAF=0.500;MQ=26.34;MQRankSum=-1.880e+00;QD=17.39;ReadPosRankSum=-7.790e-01;SOR=4.193	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,14:32:99:1|0:10136885_G_T:564,0,1422
-21	10136914	.	T	C	115.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.13;ClippingRankSum=0.548;DP=29;ExcessHet=3.0103;FS=8.158;MLEAC=1;MLEAF=0.500;MQ=27.04;MQRankSum=-1.934e+00;QD=3.99;ReadPosRankSum=0.202;SOR=2.712	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,5:29:99:0|1:10136885_G_T:123,0,1907
-21	10136915	.	G	A	34.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.77;ClippingRankSum=1.45;DP=30;ExcessHet=3.0103;FS=2.721;MLEAC=1;MLEAF=0.500;MQ=27.10;MQRankSum=-1.867e+00;QD=1.15;ReadPosRankSum=0.830;SOR=1.692	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:42:0|1:10136885_G_T:42,0,2016
-21	10136921	.	T	C	169.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.800e-02;ClippingRankSum=-4.930e-01;DP=30;ExcessHet=3.0103;FS=8.522;MLEAC=1;MLEAF=0.500;MQ=27.38;MQRankSum=-3.552e+00;QD=5.65;ReadPosRankSum=1.48;SOR=3.003	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,6:30:99:1|0:10136885_G_T:177,0,1642
-21	10136990	.	G	T	162.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.986;ClippingRankSum=-4.700e-02;DP=72;ExcessHet=3.0103;FS=4.636;MLEAC=1;MLEAF=0.500;MQ=31.36;MQRankSum=-8.610e-01;QD=2.26;ReadPosRankSum=-1.570e-01;SOR=1.609	GT:AD:DP:GQ:PL	0/1:61,11:72:99:170,0,2055
-21	10137042	.	C	T	3509.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.460e-01;ClippingRankSum=-5.740e-01;DP=268;ExcessHet=3.0103;FS=27.164;MLEAC=1;MLEAF=0.500;MQ=37.47;MQRankSum=-1.830e-01;QD=13.10;ReadPosRankSum=-5.200e-02;SOR=0.169	GT:AD:DP:GQ:PGT:PID:PL	0/1:177,91:268:99:0|1:10137042_C_T:3517,0,7292
-21	10137058	.	A	C	4299.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.116e+00;ClippingRankSum=-9.470e-01;DP=316;ExcessHet=3.0103;FS=23.595;MLEAC=1;MLEAF=0.500;MQ=37.39;MQRankSum=0.054;QD=13.65;ReadPosRankSum=1.81;SOR=0.227	GT:AD:DP:GQ:PGT:PID:PL	0/1:193,122:315:99:0|1:10137042_C_T:4307,0,7752
-21	10137082	.	G	GT	1435.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.741e+00;ClippingRankSum=0.697;DP=369;ExcessHet=3.0103;FS=7.091;MLEAC=1;MLEAF=0.500;MQ=37.12;MQRankSum=5.47;QD=4.93;ReadPosRankSum=0.541;SOR=0.790	GT:AD:DP:GQ:PL	0/1:202,89:351:99:1443,0,8917
-21	10137083	.	T	A	4710.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.475;ClippingRankSum=-1.082e+00;DP=367;ExcessHet=3.0103;FS=9.438;MLEAC=1;MLEAF=0.500;MQ=37.16;MQRankSum=-5.032e+00;QD=12.98;ReadPosRankSum=0.738;SOR=0.625	GT:AD:DP:GQ:PL	0/1:166,197:363:99:4718,0,5390
+21	10135272	.	T	C	96.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.74;MQRankSum=1.54;QD=16.11;SOR=2.093	GT:AD:DP:GQ:PL	0/1:3,3:6:99:104,0,117
+21	10135511	.	A	G	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.580e-01;ClippingRankSum=-1.231e+00;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQRankSum=1.23;QD=18.53;ReadPosRankSum=-3.580e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:48:100,0,48
+21	10135540	.	C	T	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQRankSum=1.23;QD=18.53;ReadPosRankSum=0.358;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:48:100,0,48
+21	10136335	.	A	G	102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=-1.281e+00;DP=18;ExcessHet=3.0103;FS=14.443;MLEAC=1;MLEAF=0.500;MQ=30.69;MQRankSum=-1.873e+00;QD=5.70;ReadPosRankSum=0.690;SOR=3.596	GT:AD:DP:GQ:PL	0/1:13,5:18:99:110,0,376
+21	10136414	.	C	G	1220.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.79;ClippingRankSum=-5.640e-01;DP=125;ExcessHet=3.0103;FS=12.383;MLEAC=1;MLEAF=0.500;MQ=30.73;MQRankSum=-3.834e+00;QD=9.84;ReadPosRankSum=-5.200e-02;SOR=3.109	GT:AD:DP:GQ:PGT:PID:PL	0/1:88,36:124:99:0|1:10136414_C_G:1228,0,3595
+21	10136415	.	A	G	1220.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176e+00;ClippingRankSum=0.300;DP=125;ExcessHet=3.0103;FS=12.233;MLEAC=1;MLEAF=0.500;MQ=30.82;MQRankSum=-3.348e+00;QD=9.84;ReadPosRankSum=0.788;SOR=3.033	GT:AD:DP:GQ:PGT:PID:PL	0/1:89,35:124:99:0|1:10136414_C_G:1228,0,3595
+21	10136435	.	A	C	1409.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.974e+00;ClippingRankSum=1.01;DP=137;ExcessHet=3.0103;FS=9.748;MLEAC=1;MLEAF=0.500;MQ=30.67;MQRankSum=-4.618e+00;QD=10.29;ReadPosRankSum=0.215;SOR=2.638	GT:AD:DP:GQ:PGT:PID:PL	0/1:97,40:137:99:0|1:10136435_A_C:1417,0,3950
+21	10136440	.	C	T	1406.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.09;ClippingRankSum=1.38;DP=139;ExcessHet=3.0103;FS=9.801;MLEAC=1;MLEAF=0.500;MQ=30.65;MQRankSum=-3.614e+00;QD=10.12;ReadPosRankSum=0.164;SOR=2.663	GT:AD:DP:GQ:PGT:PID:PL	0/1:98,41:139:99:0|1:10136435_A_C:1414,0,3980
+21	10136444	.	A	T	260.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.712e+00;ClippingRankSum=0.269;DP=141;ExcessHet=3.0103;FS=2.265;MLEAC=1;MLEAF=0.500;MQ=30.57;MQRankSum=0.752;QD=1.85;ReadPosRankSum=0.601;SOR=1.066	GT:AD:DP:GQ:PL	0/1:122,19:141:99:268,0,4274
+21	10136495	.	G	T	690.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;ClippingRankSum=0.773;DP=93;ExcessHet=3.0103;FS=4.818;MLEAC=1;MLEAF=0.500;MQ=31.61;MQRankSum=-2.310e-01;QD=7.43;ReadPosRankSum=-6.550e-01;SOR=1.939	GT:AD:DP:GQ:PGT:PID:PL	0/1:71,22:93:99:0|1:10136495_G_T:698,0,2892
+21	10136496	.	C	A	690.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.21;ClippingRankSum=-1.364e+00;DP=90;ExcessHet=3.0103;FS=4.823;MLEAC=1;MLEAF=0.500;MQ=31.69;MQRankSum=-9.060e-01;QD=7.67;ReadPosRankSum=-6.200e-01;SOR=1.915	GT:AD:DP:GQ:PGT:PID:PL	0/1:69,21:90:99:0|1:10136495_G_T:698,0,2892
+21	10136523	.	C	G	206.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;ClippingRankSum=-1.660e-01;DP=63;ExcessHet=3.0103;FS=9.814;MLEAC=1;MLEAF=0.500;MQ=32.90;MQRankSum=-1.794e+00;QD=3.28;ReadPosRankSum=-1.969e+00;SOR=2.739	GT:AD:DP:GQ:PL	0/1:51,12:63:99:214,0,1606
+21	10136538	.	A	G	32.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.435;DP=53;ExcessHet=3.0103;FS=4.987;MLEAC=1;MLEAF=0.500;MQ=33.17;MQRankSum=-1.333e+00;QD=0.62;ReadPosRankSum=-2.625e+00;SOR=2.000	GT:AD:DP:GQ:PL	0/1:47,6:53:40:40,0,1604
+21	10136562	.	T	G	302.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;ClippingRankSum=0.230;DP=43;ExcessHet=3.0103;FS=25.046;MLEAC=1;MLEAF=0.500;MQ=31.44;MQRankSum=1.12;QD=7.04;ReadPosRankSum=-2.030e-01;SOR=5.015	GT:AD:DP:GQ:PL	0/1:31,12:43:99:310,0,854
+21	10136666	.	T	A	272.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.47;ClippingRankSum=-1.267e+00;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.95;MQRankSum=2.43;QD=5.05;ReadPosRankSum=-2.100e-02;SOR=0.495	GT:AD:DP:GQ:PL	0/1:43,11:54:99:280,0,1602
+21	10136694	.	A	G	697.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.602e+00;ClippingRankSum=-6.990e-01;DP=170;ExcessHet=3.0103;FS=63.316;MLEAC=1;MLEAF=0.500;MQ=36.33;MQRankSum=-6.964e+00;QD=4.10;ReadPosRankSum=-3.300e-02;SOR=4.804	GT:AD:DP:GQ:PL	0/1:136,34:170:99:705,0,4769
+21	10136744	.	ATTT	A	707.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.45;ClippingRankSum=-2.387e+00;DP=368;ExcessHet=3.0103;FS=235.351;MLEAC=1;MLEAF=0.500;MQ=36.63;MQRankSum=-9.813e+00;QD=2.15;ReadPosRankSum=-1.963e+00;SOR=8.468	GT:AD:DP:GQ:PL	0/1:296,33:364:99:715,0,12396
+21	10136757	.	G	A	4213.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;ClippingRankSum=0.140;DP=368;ExcessHet=3.0103;FS=20.497;MLEAC=1;MLEAF=0.500;MQ=36.51;MQRankSum=-1.422e+01;QD=11.48;ReadPosRankSum=1.84;SOR=1.183	GT:AD:DP:GQ:PL	0/1:235,132:367:99:4221,0,7848
+21	10136761	.	C	T	1890.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.99;ClippingRankSum=9.000e-03;DP=350;ExcessHet=3.0103;FS=209.122;MLEAC=1;MLEAF=0.500;MQ=36.50;MQRankSum=-1.010e+01;QD=5.40;ReadPosRankSum=2.10;SOR=8.468	GT:AD:DP:GQ:PL	0/1:282,68:350:99:1898,0,11595
+21	10136776	.	T	C	2065.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.609e+00;ClippingRankSum=0.255;DP=290;ExcessHet=3.0103;FS=212.054;MLEAC=1;MLEAF=0.500;MQ=36.20;MQRankSum=-9.326e+00;QD=7.12;ReadPosRankSum=0.885;SOR=8.739	GT:AD:DP:GQ:PL	0/1:212,78:290:99:2073,0,7770
+21	10136796	.	G	A	298.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.954;ClippingRankSum=-1.300e+00;DP=228;ExcessHet=3.0103;FS=61.643;MLEAC=1;MLEAF=0.500;MQ=35.70;MQRankSum=-4.788e+00;QD=1.31;ReadPosRankSum=-2.310e+00;SOR=2.881	GT:AD:DP:GQ:PGT:PID:PL	0/1:204,24:228:99:0|1:10136796_G_A:306,0,8349
+21	10136804	.	T	G	181.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.604e+00;ClippingRankSum=0.203;DP=201;ExcessHet=3.0103;FS=39.016;MLEAC=1;MLEAF=0.500;MQ=35.61;MQRankSum=-4.861e+00;QD=0.90;ReadPosRankSum=-1.905e+00;SOR=2.079	GT:AD:DP:GQ:PGT:PID:PL	0/1:184,17:201:99:0|1:10136796_G_A:189,0,7868
+21	10136892	.	G	C	677.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.308e+00;ClippingRankSum=-5.400e-02;DP=33;ExcessHet=3.0103;FS=18.978;MLEAC=1;MLEAF=0.500;MQ=26.42;MQRankSum=-1.320e+00;QD=20.53;ReadPosRankSum=0.777;SOR=4.686	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,18:33:99:0|1:10136885_G_T:685,0,841
+21	10136897	.	A	G	556.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.030e-01;ClippingRankSum=-2.470e-01;DP=32;ExcessHet=3.0103;FS=16.234;MLEAC=1;MLEAF=0.500;MQ=26.34;MQRankSum=-1.880e+00;QD=17.39;ReadPosRankSum=-7.790e-01;SOR=4.193	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,14:32:99:1|0:10136885_G_T:564,0,1422
+21	10136914	.	T	C	115.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.13;ClippingRankSum=0.548;DP=29;ExcessHet=3.0103;FS=8.158;MLEAC=1;MLEAF=0.500;MQ=27.04;MQRankSum=-1.934e+00;QD=3.99;ReadPosRankSum=0.202;SOR=2.712	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,5:29:99:0|1:10136885_G_T:123,0,1907
+21	10136915	.	G	A	34.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.77;ClippingRankSum=1.45;DP=30;ExcessHet=3.0103;FS=2.721;MLEAC=1;MLEAF=0.500;MQ=27.10;MQRankSum=-1.867e+00;QD=1.15;ReadPosRankSum=0.830;SOR=1.692	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:42:0|1:10136885_G_T:42,0,2016
+21	10136921	.	T	C	169.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.800e-02;ClippingRankSum=-4.930e-01;DP=30;ExcessHet=3.0103;FS=8.522;MLEAC=1;MLEAF=0.500;MQ=27.38;MQRankSum=-3.552e+00;QD=5.65;ReadPosRankSum=1.48;SOR=3.003	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,6:30:99:1|0:10136885_G_T:177,0,1642
+21	10136990	.	G	T	162.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.986;ClippingRankSum=-4.700e-02;DP=72;ExcessHet=3.0103;FS=4.636;MLEAC=1;MLEAF=0.500;MQ=31.36;MQRankSum=-8.610e-01;QD=2.26;ReadPosRankSum=-1.570e-01;SOR=1.609	GT:AD:DP:GQ:PL	0/1:61,11:72:99:170,0,2055
+21	10137042	.	C	T	3509.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.460e-01;ClippingRankSum=-5.740e-01;DP=268;ExcessHet=3.0103;FS=27.164;MLEAC=1;MLEAF=0.500;MQ=37.47;MQRankSum=-1.830e-01;QD=13.10;ReadPosRankSum=-5.200e-02;SOR=0.169	GT:AD:DP:GQ:PGT:PID:PL	0/1:177,91:268:99:0|1:10137042_C_T:3517,0,7292
+21	10137058	.	A	C	4299.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.116e+00;ClippingRankSum=-9.470e-01;DP=316;ExcessHet=3.0103;FS=23.595;MLEAC=1;MLEAF=0.500;MQ=37.39;MQRankSum=0.054;QD=13.65;ReadPosRankSum=1.81;SOR=0.227	GT:AD:DP:GQ:PGT:PID:PL	0/1:193,122:315:99:0|1:10137042_C_T:4307,0,7752
+21	10137082	.	G	GT	1435.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.741e+00;ClippingRankSum=0.697;DP=369;ExcessHet=3.0103;FS=7.091;MLEAC=1;MLEAF=0.500;MQ=37.12;MQRankSum=5.47;QD=4.93;ReadPosRankSum=0.541;SOR=0.790	GT:AD:DP:GQ:PL	0/1:202,89:351:99:1443,0,8917
+21	10137083	.	T	A	4710.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.475;ClippingRankSum=-1.082e+00;DP=367;ExcessHet=3.0103;FS=9.438;MLEAC=1;MLEAF=0.500;MQ=37.16;MQRankSum=-5.032e+00;QD=12.98;ReadPosRankSum=0.738;SOR=0.625	GT:AD:DP:GQ:PL	0/1:166,197:363:99:4718,0,5390
 21	10137112	.	GT	G	2360.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.86;ClippingRankSum=1.47;DP=255;ExcessHet=3.0103;FS=1.706;MLEAC=1;MLEAF=0.500;MQ=36.71;MQRankSum=-2.561e+00;QD=10.78;ReadPosRankSum=1.47;SOR=0.826	GT:AD:DP:GQ:PL	0/1:139,80:219:99:2368,0,4687
-21	10137117	.	T	C	844.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.357e+00;ClippingRankSum=0.464;DP=232;ExcessHet=3.0103;FS=1.358;MLEAC=1;MLEAF=0.500;MQ=36.67;MQRankSum=-2.740e-01;QD=3.64;ReadPosRankSum=1.69;SOR=0.843	GT:AD:DP:GQ:PL	0/1:191,41:232:99:852,0,7573
-21	10137130	.	A	G	4153.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.680e-01;ClippingRankSum=-3.780e-01;DP=182;ExcessHet=3.0103;FS=0.555;MLEAC=1;MLEAF=0.500;MQ=36.17;MQRankSum=-5.233e+00;QD=22.82;ReadPosRankSum=2.16;SOR=0.639	GT:AD:DP:GQ:PL	0/1:72,110:182:99:4161,0,2349
-21	10137256	.	A	G	223.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.860e-01;ClippingRankSum=-8.290e-01;DP=33;ExcessHet=3.0103;FS=18.248;MLEAC=1;MLEAF=0.500;MQ=35.70;MQRankSum=-1.839e+00;QD=6.78;ReadPosRankSum=-7.880e-01;SOR=4.310	GT:AD:DP:GQ:PL	0/1:24,9:33:99:231,0,809
-21	10137354	.	C	G	2861.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.566;ClippingRankSum=0.189;DP=131;ExcessHet=3.0103;FS=95.647;MLEAC=1;MLEAF=0.500;MQ=32.55;MQRankSum=-7.680e-01;QD=21.84;ReadPosRankSum=2.31;SOR=8.376	GT:AD:DP:GQ:PL	0/1:39,92:131:99:2869,0,916
-21	10137360	.	G	A	130.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.12;ClippingRankSum=0.161;DP=141;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=32.17;MQRankSum=0.111;QD=0.93;ReadPosRankSum=0.674;SOR=2.061	GT:AD:DP:GQ:PL	0/1:124,17:141:99:138,0,4211
-21	10137407	.	C	T	2017.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.300e-02;ClippingRankSum=1.04;DP=124;ExcessHet=3.0103;FS=27.502;MLEAC=1;MLEAF=0.500;MQ=32.58;MQRankSum=-2.271e+00;QD=16.27;ReadPosRankSum=-2.860e-01;SOR=5.089	GT:AD:DP:GQ:PL	0/1:52,72:124:99:2025,0,1471
-21	10137495	.	T	C	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-9.780e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.31;MQRankSum=0.382;QD=6.15;ReadPosRankSum=-5.660e-01;SOR=0.693	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,238
+21	10137117	.	T	C	844.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.357e+00;ClippingRankSum=0.464;DP=232;ExcessHet=3.0103;FS=1.358;MLEAC=1;MLEAF=0.500;MQ=36.67;MQRankSum=-2.740e-01;QD=3.64;ReadPosRankSum=1.69;SOR=0.843	GT:AD:DP:GQ:PL	0/1:191,41:232:99:852,0,7573
+21	10137130	.	A	G	4153.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.680e-01;ClippingRankSum=-3.780e-01;DP=182;ExcessHet=3.0103;FS=0.555;MLEAC=1;MLEAF=0.500;MQ=36.17;MQRankSum=-5.233e+00;QD=22.82;ReadPosRankSum=2.16;SOR=0.639	GT:AD:DP:GQ:PL	0/1:72,110:182:99:4161,0,2349
+21	10137256	.	A	G	223.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.860e-01;ClippingRankSum=-8.290e-01;DP=33;ExcessHet=3.0103;FS=18.248;MLEAC=1;MLEAF=0.500;MQ=35.70;MQRankSum=-1.839e+00;QD=6.78;ReadPosRankSum=-7.880e-01;SOR=4.310	GT:AD:DP:GQ:PL	0/1:24,9:33:99:231,0,809
+21	10137354	.	C	G	2861.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.566;ClippingRankSum=0.189;DP=131;ExcessHet=3.0103;FS=95.647;MLEAC=1;MLEAF=0.500;MQ=32.55;MQRankSum=-7.680e-01;QD=21.84;ReadPosRankSum=2.31;SOR=8.376	GT:AD:DP:GQ:PL	0/1:39,92:131:99:2869,0,916
+21	10137360	.	G	A	130.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.12;ClippingRankSum=0.161;DP=141;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=32.17;MQRankSum=0.111;QD=0.93;ReadPosRankSum=0.674;SOR=2.061	GT:AD:DP:GQ:PL	0/1:124,17:141:99:138,0,4211
+21	10137407	.	C	T	2017.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.300e-02;ClippingRankSum=1.04;DP=124;ExcessHet=3.0103;FS=27.502;MLEAC=1;MLEAF=0.500;MQ=32.58;MQRankSum=-2.271e+00;QD=16.27;ReadPosRankSum=-2.860e-01;SOR=5.089	GT:AD:DP:GQ:PL	0/1:52,72:124:99:2025,0,1471
+21	10137495	.	T	C	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-9.780e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.31;MQRankSum=0.382;QD=6.15;ReadPosRankSum=-5.660e-01;SOR=0.693	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,238
 21	10138457	.	TC	T	465.61	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.373;ClippingRankSum=0.373;DP=18;ExcessHet=3.0103;FS=9.294;MLEAC=1;MLEAF=0.500;MQ=23.29;MQRankSum=0.522;QD=27.39;ReadPosRankSum=-1.714e+00;SOR=5.549	GT:AD:DP:GQ:PL	0/1:2,15:17:20:473,0,20
-21	10138530	.	G	C	476.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.73;ClippingRankSum=0.572;DP=54;ExcessHet=3.0103;FS=34.781;MLEAC=1;MLEAF=0.500;MQ=30.15;MQRankSum=-2.597e+00;QD=8.83;ReadPosRankSum=2.21;SOR=5.561	GT:AD:DP:GQ:PL	0/1:32,22:54:99:484,0,808
-21	10138577	.	T	C	149.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.240e-01;ClippingRankSum=-5.920e-01;DP=53;ExcessHet=3.0103;FS=31.729;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-7.080e-01;QD=2.88;ReadPosRankSum=1.54;SOR=4.799	GT:AD:DP:GQ:PL	0/1:42,10:52:99:157,0,1307
-21	10138629	.	A	G	36.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.39;ClippingRankSum=0.737;DP=67;ExcessHet=3.0103;FS=7.290;MLEAC=1;MLEAF=0.500;MQ=27.47;MQRankSum=0.167;QD=0.55;ReadPosRankSum=0.324;SOR=2.303	GT:AD:DP:GQ:PL	0/1:58,8:66:44:44,0,1659
-21	10138683	.	G	A	145.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=1.11;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.93;MQRankSum=-1.800e-01;QD=3.17;ReadPosRankSum=0.953;SOR=0.105	GT:AD:DP:GQ:PL	0/1:35,11:46:99:153,0,788
-21	10138775	.	C	A	101.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.47;ClippingRankSum=-1.350e-01;DP=99;ExcessHet=3.0103;FS=11.161;MLEAC=1;MLEAF=0.500;MQ=24.70;MQRankSum=1.28;QD=1.09;ReadPosRankSum=-3.180e-01;SOR=0.889	GT:AD:DP:GQ:PL	0/1:79,14:99:99:109,0,2014
-21	10138776	.	G	A	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.49;ClippingRankSum=-1.473e+00;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.59;MQRankSum=2.98;QD=0.35;ReadPosRankSum=-9.970e-01;SOR=0.879	GT:AD:DP:GQ:PL	0/1:97,9:106:45:45,0,2627
-21	10138978	.	A	C	56.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656e+00;ClippingRankSum=0.193;DP=219;ExcessHet=3.0103;FS=2.624;MLEAC=1;MLEAF=0.500;MQ=22.41;MQRankSum=0.889;QD=0.26;ReadPosRankSum=1.03;SOR=0.727	GT:AD:DP:GQ:PL	0/1:191,28:219:64:64,0,4422
-21	10139076	.	G	C	147.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.101;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.24;MQRankSum=-7.100e-01;QD=4.34;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,8:34:99:0|1:10139060_C_T:155,0,593
-21	10139164	.	A	G	1212.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.473e+00;ClippingRankSum=-1.610e-01;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.77;MQRankSum=0.395;QD=16.61;ReadPosRankSum=1.58;SOR=0.481	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,32:73:99:0|1:10139164_A_G:1220,0,1654
-21	10139165	.	G	A	1212.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.47;ClippingRankSum=0.784;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.77;MQRankSum=0.128;QD=16.61;ReadPosRankSum=1.57;SOR=0.481	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,32:73:99:0|1:10139164_A_G:1220,0,1654
-21	10139199	.	G	A	45.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.770e-01;ClippingRankSum=0.091;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.42;MQRankSum=1.49;QD=0.86;ReadPosRankSum=1.14;SOR=0.063	GT:AD:DP:GQ:PL	0/1:46,7:57:53:53,0,1156
-21	10139271	.	C	A	183.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.088e+00;ClippingRankSum=0.516;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.55;MQRankSum=0.439;QD=5.56;ReadPosRankSum=-1.279e+00;SOR=0.241	GT:AD:DP:GQ:PL	0/1:22,11:33:99:191,0,477
-21	10139335	.	G	A	37.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;QD=18.64;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-21	10139408	.	A	C	203.98	.	AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.00;QD=29.14;SOR=4.174	GT:AD:DP:GQ:PL	1/1:0,7:7:21:218,21,0
-21	10139538	.	C	T	62.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.25;ClippingRankSum=-2.017e+00;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.54;MQRankSum=3.38;QD=2.41;ReadPosRankSum=-7.810e-01;SOR=0.072	GT:AD:DP:GQ:PL	0/1:21,5:26:70:70,0,481
-21	10139700	.	C	T	127.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.28;ClippingRankSum=-2.600e-01;DP=26;ExcessHet=3.0103;FS=21.535;MLEAC=1;MLEAF=0.500;MQ=25.28;MQRankSum=2.41;QD=4.91;ReadPosRankSum=3.06;SOR=3.589	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,5:26:99:0|1:10139700_C_T:135,0,1035
-21	10139710	.	G	T	55.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=-3.790e-01;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.21;MQRankSum=2.63;QD=1.21;ReadPosRankSum=2.63;SOR=0.838	GT:AD:DP:GQ:PL	0/1:41,5:50:63:63,0,1880
-21	10139711	.	G	A	54.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.98;ClippingRankSum=0.396;DP=51;ExcessHet=3.0103;FS=12.802;MLEAC=1;MLEAF=0.500;MQ=24.14;MQRankSum=3.15;QD=1.07;ReadPosRankSum=3.47;SOR=3.607	GT:AD:DP:GQ:PGT:PID:PL	0/1:46,5:51:62:0|1:10139700_C_T:62,0,1991
-21	10139712	.	C	A	54.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=-6.570e-01;DP=54;ExcessHet=3.0103;FS=12.850;MLEAC=1;MLEAF=0.500;MQ=24.08;MQRankSum=3.19;QD=1.01;ReadPosRankSum=3.49;SOR=3.605	GT:AD:DP:GQ:PGT:PID:PL	0/1:49,5:54:62:0|1:10139700_C_T:62,0,1991
-21	10139726	.	G	A	91.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.338;ClippingRankSum=0.627;DP=87;ExcessHet=3.0103;FS=1.195;MLEAC=1;MLEAF=0.500;MQ=23.75;MQRankSum=-5.550e-01;QD=1.07;ReadPosRankSum=-1.013e+00;SOR=0.418	GT:AD:DP:GQ:PL	0/1:73,13:86:99:99,0,1953
-21	10139739	.	C	T	68.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.24;ClippingRankSum=-9.530e-01;DP=130;ExcessHet=3.0103;FS=13.563;MLEAC=1;MLEAF=0.500;MQ=23.91;MQRankSum=0.098;QD=0.58;ReadPosRankSum=0.109;SOR=0.568	GT:AD:DP:GQ:PL	0/1:103,16:130:76:76,0,2859
-21	10139997	.	G	A	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;ClippingRankSum=-1.560e-01;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.34;MQRankSum=-3.110e-01;QD=2.69;ReadPosRankSum=1.87;SOR=1.426	GT:AD:DP:GQ:PL	0/1:11,3:14:45:45,0,262
-21	10140064	.	T	A	151.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.130e+00;ClippingRankSum=0.858;DP=27;ExcessHet=3.0103;FS=11.666;MLEAC=1;MLEAF=0.500;MQ=30.31;MQRankSum=-1.743e+00;QD=5.61;ReadPosRankSum=-1.024e+00;SOR=3.456	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,7:27:99:0|1:10140064_T_A:159,0,865
-21	10140082	.	C	T	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.04;ClippingRankSum=-9.680e-01;DP=30;ExcessHet=3.0103;FS=2.741;MLEAC=1;MLEAF=0.500;MQ=30.11;MQRankSum=1.11;QD=1.25;ReadPosRankSum=2.01;SOR=1.942	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:45:0|1:10140064_T_A:45,0,1045
-21	10140212	.	C	A	623.03	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.96;QD=27.09;SOR=1.426	GT:AD:DP:GQ:PL	1/1:0,23:23:69:637,69,0
-21	10140602	.	G	T	249.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.94;ClippingRankSum=0.387;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.49;MQRankSum=1.80;QD=4.54;ReadPosRankSum=-2.690e-01;SOR=0.360	GT:AD:DP:GQ:PL	0/1:40,15:66:99:257,0,903
-21	10140687	.	A	G	260.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;ClippingRankSum=-6.150e-01;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.67;MQRankSum=-1.460e-01;QD=10.86;ReadPosRankSum=1.67;SOR=0.430	GT:AD:DP:GQ:PL	0/1:14,10:24:99:268,0,316
-21	10140740	.	G	T	63.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.12;ClippingRankSum=-2.170e-01;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.15;MQRankSum=-4.170e-01;QD=1.41;ReadPosRankSum=-1.653e+00;SOR=0.030	GT:AD:DP:GQ:PL	0/1:39,6:45:71:71,0,1333
-21	10140748	.	T	A	214.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.820e+00;ClippingRankSum=-4.940e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.40;MQRankSum=0.978;QD=3.90;ReadPosRankSum=0.095;SOR=0.069	GT:AD:DP:GQ:PL	0/1:44,11:55:99:222,0,1448
-21	10140845	.	T	G	242.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.060;ClippingRankSum=-1.002e+00;DP=380;ExcessHet=3.0103;FS=4.597;MLEAC=1;MLEAF=0.500;MQ=39.73;MQRankSum=-8.580e-01;QD=0.64;ReadPosRankSum=0.955;SOR=0.390	GT:AD:DP:GQ:PL	0/1:338,41:379:99:250,0,11515
+21	10138530	.	G	C	476.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.73;ClippingRankSum=0.572;DP=54;ExcessHet=3.0103;FS=34.781;MLEAC=1;MLEAF=0.500;MQ=30.15;MQRankSum=-2.597e+00;QD=8.83;ReadPosRankSum=2.21;SOR=5.561	GT:AD:DP:GQ:PL	0/1:32,22:54:99:484,0,808
+21	10138577	.	T	C	149.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.240e-01;ClippingRankSum=-5.920e-01;DP=53;ExcessHet=3.0103;FS=31.729;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-7.080e-01;QD=2.88;ReadPosRankSum=1.54;SOR=4.799	GT:AD:DP:GQ:PL	0/1:42,10:52:99:157,0,1307
+21	10138629	.	A	G	36.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.39;ClippingRankSum=0.737;DP=67;ExcessHet=3.0103;FS=7.290;MLEAC=1;MLEAF=0.500;MQ=27.47;MQRankSum=0.167;QD=0.56;ReadPosRankSum=0.324;SOR=2.303	GT:AD:DP:GQ:PL	0/1:58,8:66:44:44,0,1659
+21	10138683	.	G	A	145.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=1.11;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.93;MQRankSum=-1.800e-01;QD=3.17;ReadPosRankSum=0.953;SOR=0.105	GT:AD:DP:GQ:PL	0/1:35,11:46:99:153,0,788
+21	10138775	.	C	A	101.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.47;ClippingRankSum=-1.350e-01;DP=99;ExcessHet=3.0103;FS=11.161;MLEAC=1;MLEAF=0.500;MQ=24.70;MQRankSum=1.28;QD=1.09;ReadPosRankSum=-3.180e-01;SOR=0.889	GT:AD:DP:GQ:PL	0/1:79,14:99:99:109,0,2014
+21	10138776	.	G	A	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.49;ClippingRankSum=-1.473e+00;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.59;MQRankSum=2.98;QD=0.36;ReadPosRankSum=-9.970e-01;SOR=0.879	GT:AD:DP:GQ:PL	0/1:97,9:106:45:45,0,2627
+21	10138978	.	A	C	56.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656e+00;ClippingRankSum=0.193;DP=219;ExcessHet=3.0103;FS=2.624;MLEAC=1;MLEAF=0.500;MQ=22.41;MQRankSum=0.889;QD=0.26;ReadPosRankSum=1.03;SOR=0.727	GT:AD:DP:GQ:PL	0/1:191,28:219:64:64,0,4422
+21	10139076	.	G	C	147.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.101;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.24;MQRankSum=-7.100e-01;QD=4.34;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,8:34:99:0|1:10139060_C_T:155,0,593
+21	10139164	.	A	G	1212.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.473e+00;ClippingRankSum=-1.610e-01;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.77;MQRankSum=0.395;QD=16.61;ReadPosRankSum=1.58;SOR=0.481	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,32:73:99:0|1:10139164_A_G:1220,0,1654
+21	10139165	.	G	A	1212.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.47;ClippingRankSum=0.784;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.77;MQRankSum=0.128;QD=16.61;ReadPosRankSum=1.57;SOR=0.481	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,32:73:99:0|1:10139164_A_G:1220,0,1654
+21	10139199	.	G	A	45.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.770e-01;ClippingRankSum=0.091;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.42;MQRankSum=1.49;QD=0.86;ReadPosRankSum=1.14;SOR=0.063	GT:AD:DP:GQ:PL	0/1:46,7:57:53:53,0,1156
+21	10139271	.	C	A	183.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.088e+00;ClippingRankSum=0.516;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.55;MQRankSum=0.439;QD=5.56;ReadPosRankSum=-1.279e+00;SOR=0.241	GT:AD:DP:GQ:PL	0/1:22,11:33:99:191,0,477
+21	10139335	.	G	A	37.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;QD=18.66;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
+21	10139408	.	A	C	204.02	.	AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.00;QD=29.15;SOR=4.174	GT:AD:DP:GQ:PL	1/1:0,7:7:21:218,21,0
+21	10139538	.	C	T	62.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.25;ClippingRankSum=-2.017e+00;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.54;MQRankSum=3.38;QD=2.41;ReadPosRankSum=-7.810e-01;SOR=0.072	GT:AD:DP:GQ:PL	0/1:21,5:26:70:70,0,481
+21	10139700	.	C	T	127.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.28;ClippingRankSum=-2.600e-01;DP=26;ExcessHet=3.0103;FS=21.535;MLEAC=1;MLEAF=0.500;MQ=25.28;MQRankSum=2.41;QD=4.91;ReadPosRankSum=3.06;SOR=3.589	GT:AD:DP:GQ:PGT:PID:PL	0/1:21,5:26:99:0|1:10139700_C_T:135,0,1035
+21	10139710	.	G	T	55.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=-3.790e-01;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.21;MQRankSum=2.63;QD=1.21;ReadPosRankSum=2.63;SOR=0.838	GT:AD:DP:GQ:PL	0/1:41,5:50:63:63,0,1880
+21	10139711	.	G	A	54.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.98;ClippingRankSum=0.396;DP=51;ExcessHet=3.0103;FS=12.802;MLEAC=1;MLEAF=0.500;MQ=24.14;MQRankSum=3.15;QD=1.07;ReadPosRankSum=3.47;SOR=3.607	GT:AD:DP:GQ:PGT:PID:PL	0/1:46,5:51:62:0|1:10139700_C_T:62,0,1991
+21	10139712	.	C	A	54.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=-6.570e-01;DP=54;ExcessHet=3.0103;FS=12.850;MLEAC=1;MLEAF=0.500;MQ=24.08;MQRankSum=3.19;QD=1.01;ReadPosRankSum=3.49;SOR=3.605	GT:AD:DP:GQ:PGT:PID:PL	0/1:49,5:54:62:0|1:10139700_C_T:62,0,1991
+21	10139726	.	G	A	91.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.338;ClippingRankSum=0.627;DP=87;ExcessHet=3.0103;FS=1.195;MLEAC=1;MLEAF=0.500;MQ=23.75;MQRankSum=-5.550e-01;QD=1.07;ReadPosRankSum=-1.013e+00;SOR=0.418	GT:AD:DP:GQ:PL	0/1:73,13:86:99:99,0,1953
+21	10139739	.	C	T	68.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.24;ClippingRankSum=-9.530e-01;DP=130;ExcessHet=3.0103;FS=13.563;MLEAC=1;MLEAF=0.500;MQ=23.91;MQRankSum=0.098;QD=0.58;ReadPosRankSum=0.109;SOR=0.568	GT:AD:DP:GQ:PL	0/1:103,16:130:76:76,0,2859
+21	10139997	.	G	A	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;ClippingRankSum=-1.560e-01;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.34;MQRankSum=-3.110e-01;QD=2.69;ReadPosRankSum=1.87;SOR=1.426	GT:AD:DP:GQ:PL	0/1:11,3:14:45:45,0,262
+21	10140064	.	T	A	151.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.130e+00;ClippingRankSum=0.858;DP=27;ExcessHet=3.0103;FS=11.666;MLEAC=1;MLEAF=0.500;MQ=30.31;MQRankSum=-1.743e+00;QD=5.62;ReadPosRankSum=-1.024e+00;SOR=3.456	GT:AD:DP:GQ:PGT:PID:PL	0/1:20,7:27:99:0|1:10140064_T_A:159,0,865
+21	10140082	.	C	T	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.04;ClippingRankSum=-9.680e-01;DP=30;ExcessHet=3.0103;FS=2.741;MLEAC=1;MLEAF=0.500;MQ=30.11;MQRankSum=1.11;QD=1.25;ReadPosRankSum=2.01;SOR=1.942	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,3:30:45:0|1:10140064_T_A:45,0,1045
+21	10140212	.	C	A	623.06	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.96;QD=27.09;SOR=1.426	GT:AD:DP:GQ:PL	1/1:0,23:23:69:637,69,0
+21	10140602	.	G	T	249.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.94;ClippingRankSum=0.387;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.49;MQRankSum=1.80;QD=4.54;ReadPosRankSum=-2.690e-01;SOR=0.360	GT:AD:DP:GQ:PL	0/1:40,15:66:99:257,0,903
+21	10140687	.	A	G	260.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;ClippingRankSum=-6.150e-01;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.67;MQRankSum=-1.460e-01;QD=10.86;ReadPosRankSum=1.67;SOR=0.430	GT:AD:DP:GQ:PL	0/1:14,10:24:99:268,0,316
+21	10140740	.	G	T	63.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.12;ClippingRankSum=-2.170e-01;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.15;MQRankSum=-4.170e-01;QD=1.41;ReadPosRankSum=-1.653e+00;SOR=0.030	GT:AD:DP:GQ:PL	0/1:39,6:45:71:71,0,1333
+21	10140748	.	T	A	214.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.820e+00;ClippingRankSum=-4.940e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.40;MQRankSum=0.978;QD=3.90;ReadPosRankSum=0.095;SOR=0.069	GT:AD:DP:GQ:PL	0/1:44,11:55:99:222,0,1448
+21	10140845	.	T	G	242.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.060;ClippingRankSum=-1.002e+00;DP=380;ExcessHet=3.0103;FS=4.597;MLEAC=1;MLEAF=0.500;MQ=39.73;MQRankSum=-8.580e-01;QD=0.64;ReadPosRankSum=0.955;SOR=0.390	GT:AD:DP:GQ:PL	0/1:338,41:379:99:250,0,11515
 21	10140868	.	CT	C	965.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.829e+00;ClippingRankSum=0.084;DP=471;ExcessHet=3.0103;FS=3.571;MLEAC=1;MLEAF=0.500;MQ=40.98;MQRankSum=-1.203e+00;QD=2.22;ReadPosRankSum=-1.400e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:376,59:460:99:973,0,14660
-21	10140909	.	C	T	1652.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.79;ClippingRankSum=2.08;DP=499;ExcessHet=3.0103;FS=5.542;MLEAC=1;MLEAF=0.500;MQ=41.64;MQRankSum=-1.485e+00;QD=3.32;ReadPosRankSum=0.977;SOR=0.958	GT:AD:DP:GQ:PL	0/1:401,97:498:99:1660,0,12258
-21	10140935	.	C	T	3758.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=7.86;ClippingRankSum=1.32;DP=375;ExcessHet=3.0103;FS=12.737;MLEAC=1;MLEAF=0.500;MQ=39.75;MQRankSum=-5.580e-01;QD=10.05;ReadPosRankSum=-9.110e-01;SOR=0.765	GT:AD:DP:GQ:PL	0/1:238,136:374:99:3766,0,6725
-21	10141032	.	T	C	270.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.021e+00;ClippingRankSum=-8.320e-01;DP=51;ExcessHet=3.0103;FS=10.184;MLEAC=1;MLEAF=0.500;MQ=27.09;MQRankSum=2.50;QD=5.31;ReadPosRankSum=-1.400e-01;SOR=2.863	GT:AD:DP:GQ:PL	0/1:38,13:51:99:278,0,976
-21	10141075	.	A	C	668.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.028e+00;ClippingRankSum=-4.700e-01;DP=205;ExcessHet=3.0103;FS=2.447;MLEAC=1;MLEAF=0.500;MQ=39.05;MQRankSum=1.45;QD=3.28;ReadPosRankSum=-7.630e-01;SOR=0.978	GT:AD:DP:GQ:PL	0/1:171,33:204:99:676,0,6218
-21	10141076	.	G	A	90.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.60;ClippingRankSum=0.654;DP=208;ExcessHet=3.0103;FS=10.517;MLEAC=1;MLEAF=0.500;MQ=38.99;MQRankSum=1.52;QD=0.44;ReadPosRankSum=-1.260e+00;SOR=1.828	GT:AD:DP:GQ:PL	0/1:190,18:208:98:98,0,7860
-21	10141097	.	C	T	701.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.740e-01;ClippingRankSum=-2.890e-01;DP=313;ExcessHet=3.0103;FS=0.611;MLEAC=1;MLEAF=0.500;MQ=40.58;MQRankSum=1.08;QD=2.24;ReadPosRankSum=-5.180e-01;SOR=0.618	GT:AD:DP:GQ:PL	0/1:271,42:313:99:709,0,10290
-21	10141118	.	G	T	686.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.45;ClippingRankSum=-3.050e-01;DP=424;ExcessHet=3.0103;FS=0.832;MLEAC=1;MLEAF=0.500;MQ=41.41;MQRankSum=-1.298e+00;QD=1.62;ReadPosRankSum=0.510;SOR=0.597	GT:AD:DP:GQ:PL	0/1:372,51:423:99:694,0,14702
+21	10140909	.	C	T	1652.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.79;ClippingRankSum=2.08;DP=499;ExcessHet=3.0103;FS=5.542;MLEAC=1;MLEAF=0.500;MQ=41.64;MQRankSum=-1.485e+00;QD=3.32;ReadPosRankSum=0.977;SOR=0.958	GT:AD:DP:GQ:PL	0/1:401,97:498:99:1660,0,12258
+21	10140935	.	C	T	3758.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=7.86;ClippingRankSum=1.32;DP=375;ExcessHet=3.0103;FS=12.737;MLEAC=1;MLEAF=0.500;MQ=39.75;MQRankSum=-5.580e-01;QD=10.05;ReadPosRankSum=-9.110e-01;SOR=0.765	GT:AD:DP:GQ:PL	0/1:238,136:374:99:3766,0,6725
+21	10141032	.	T	C	270.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.021e+00;ClippingRankSum=-8.320e-01;DP=51;ExcessHet=3.0103;FS=10.184;MLEAC=1;MLEAF=0.500;MQ=27.09;MQRankSum=2.50;QD=5.31;ReadPosRankSum=-1.400e-01;SOR=2.863	GT:AD:DP:GQ:PL	0/1:38,13:51:99:278,0,976
+21	10141075	.	A	C	668.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.028e+00;ClippingRankSum=-4.700e-01;DP=205;ExcessHet=3.0103;FS=2.447;MLEAC=1;MLEAF=0.500;MQ=39.05;MQRankSum=1.45;QD=3.28;ReadPosRankSum=-7.630e-01;SOR=0.978	GT:AD:DP:GQ:PL	0/1:171,33:204:99:676,0,6218
+21	10141076	.	G	A	90.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.60;ClippingRankSum=0.654;DP=208;ExcessHet=3.0103;FS=10.517;MLEAC=1;MLEAF=0.500;MQ=38.99;MQRankSum=1.52;QD=0.44;ReadPosRankSum=-1.260e+00;SOR=1.828	GT:AD:DP:GQ:PL	0/1:190,18:208:98:98,0,7860
+21	10141097	.	C	T	701.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.740e-01;ClippingRankSum=-2.890e-01;DP=313;ExcessHet=3.0103;FS=0.611;MLEAC=1;MLEAF=0.500;MQ=40.58;MQRankSum=1.08;QD=2.24;ReadPosRankSum=-5.180e-01;SOR=0.618	GT:AD:DP:GQ:PL	0/1:271,42:313:99:709,0,10290
+21	10141118	.	G	T	686.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.45;ClippingRankSum=-3.050e-01;DP=424;ExcessHet=3.0103;FS=0.832;MLEAC=1;MLEAF=0.500;MQ=41.41;MQRankSum=-1.298e+00;QD=1.62;ReadPosRankSum=0.510;SOR=0.597	GT:AD:DP:GQ:PL	0/1:372,51:423:99:694,0,14702
 21	10141119	.	TA	T	3413.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.136;ClippingRankSum=-1.307e+00;DP=443;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.63;MQRankSum=1.17;QD=8.33;ReadPosRankSum=1.62;SOR=0.662	GT:AD:DP:GQ:PL	0/1:245,165:430:99:3421,0,8500
-21	10141131	.	C	T	1348.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.309;ClippingRankSum=1.11;DP=529;ExcessHet=3.0103;FS=1.650;MLEAC=1;MLEAF=0.500;MQ=42.65;MQRankSum=0.190;QD=2.55;ReadPosRankSum=-1.988e+00;SOR=0.932	GT:AD:DP:GQ:PL	0/1:452,77:529:99:1356,0,17656
-21	10141173	.	G	C	2666.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.528;ClippingRankSum=0.683;DP=646;ExcessHet=3.0103;FS=2.441;MLEAC=1;MLEAF=0.500;MQ=44.17;MQRankSum=-7.530e-01;QD=4.13;ReadPosRankSum=1.17;SOR=0.476	GT:AD:DP:GQ:PL	0/1:530,115:645:99:2674,0,19600
+21	10141131	.	C	T	1348.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.309;ClippingRankSum=1.11;DP=529;ExcessHet=3.0103;FS=1.650;MLEAC=1;MLEAF=0.500;MQ=42.65;MQRankSum=0.190;QD=2.55;ReadPosRankSum=-1.988e+00;SOR=0.932	GT:AD:DP:GQ:PL	0/1:452,77:529:99:1356,0,17656
+21	10141173	.	G	C	2666.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.528;ClippingRankSum=0.683;DP=646;ExcessHet=3.0103;FS=2.441;MLEAC=1;MLEAF=0.500;MQ=44.17;MQRankSum=-7.530e-01;QD=4.13;ReadPosRankSum=1.17;SOR=0.476	GT:AD:DP:GQ:PL	0/1:530,115:645:99:2674,0,19600
 21	10141189	.	TAA	T	739.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.13;ClippingRankSum=0.043;DP=632;ExcessHet=3.0103;FS=3.386;MLEAC=1;MLEAF=0.500;MQ=44.18;MQRankSum=-4.610e-01;QD=1.18;ReadPosRankSum=3.26;SOR=0.707	GT:AD:DP:GQ:PL	0/1:570,59:629:99:747,0,23833
-21	10141275	.	G	A	823.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=-1.072e+00;DP=192;ExcessHet=3.0103;FS=2.122;MLEAC=1;MLEAF=0.500;MQ=39.97;MQRankSum=-6.555e+00;QD=4.29;ReadPosRankSum=1.45;SOR=0.896	GT:AD:DP:GQ:PL	0/1:144,48:192:99:831,0,4727
-21	10141304	.	C	A	3725.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.74;ClippingRankSum=-1.400e-01;DP=156;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=34.84;MQRankSum=-1.962e+00;QD=23.88;ReadPosRankSum=0.996;SOR=0.833	GT:AD:DP:GQ:PL	0/1:26,130:156:99:3733,0,508
-21	10141315	.	T	C	3693.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.661e+00;ClippingRankSum=-8.760e-01;DP=135;ExcessHet=3.0103;FS=3.354;MLEAC=1;MLEAF=0.500;MQ=33.43;MQRankSum=-1.395e+00;QD=27.36;ReadPosRankSum=-7.620e-01;SOR=0.381	GT:AD:DP:GQ:PL	0/1:19,116:135:99:3701,0,303
-21	10141318	.	C	G	719.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.240e-01;ClippingRankSum=0.129;DP=133;ExcessHet=3.0103;FS=9.719;MLEAC=1;MLEAF=0.500;MQ=33.35;MQRankSum=3.29;QD=5.41;ReadPosRankSum=8.000e-03;SOR=1.447	GT:AD:DP:GQ:PL	0/1:101,32:133:99:727,0,3058
-21	10141336	.	A	C	3056.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.600e-02;ClippingRankSum=0.317;DP=121;ExcessHet=3.0103;FS=7.047;MLEAC=1;MLEAF=0.500;MQ=32.61;MQRankSum=-9.140e-01;QD=25.26;ReadPosRankSum=-4.960e-01;SOR=0.922	GT:AD:DP:GQ:PL	0/1:17,104:121:99:3064,0,227
-21	10141374	.	T	C	2963.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;ClippingRankSum=-1.190e-01;DP=159;ExcessHet=3.0103;FS=21.794;MLEAC=1;MLEAF=0.500;MQ=34.24;MQRankSum=-2.720e-01;QD=18.64;ReadPosRankSum=0.031;SOR=1.204	GT:AD:DP:GQ:PL	0/1:53,106:159:99:2971,0,1606
-21	10141384	.	C	T	5509.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.12;ClippingRankSum=-2.630e-01;DP=168;ExcessHet=3.0103;FS=30.993;MLEAC=1;MLEAF=0.500;MQ=35.19;MQRankSum=1.20;QD=32.80;ReadPosRankSum=-2.050e-01;SOR=1.493	GT:AD:DP:GQ:PL	0/1:30,138:168:99:5517,0,585
-21	10141459	.	G	C	657.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.51;ClippingRankSum=-5.850e-01;DP=299;ExcessHet=3.0103;FS=18.034;MLEAC=1;MLEAF=0.500;MQ=31.64;MQRankSum=-4.960e-01;QD=2.21;ReadPosRankSum=1.14;SOR=2.629	GT:AD:DP:GQ:PL	0/1:257,40:297:99:665,0,8998
-21	10141464	.	C	G	589.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.044;ClippingRankSum=0.355;DP=298;ExcessHet=3.0103;FS=23.693;MLEAC=1;MLEAF=0.500;MQ=31.15;MQRankSum=-1.283e+00;QD=1.99;ReadPosRankSum=0.698;SOR=4.082	GT:AD:DP:GQ:PL	0/1:261,35:296:99:597,0,11007
-21	10141467	.	G	C	605.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.00;ClippingRankSum=0.044;DP=298;ExcessHet=3.0103;FS=35.719;MLEAC=1;MLEAF=0.500;MQ=31.13;MQRankSum=-2.625e+00;QD=2.17;ReadPosRankSum=1.40;SOR=4.804	GT:AD:DP:GQ:PL	0/1:246,33:296:99:613,0,10387
-21	10141513	.	A	T	137.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.520e-01;ClippingRankSum=0.373;DP=255;ExcessHet=3.0103;FS=17.023;MLEAC=1;MLEAF=0.500;MQ=34.23;MQRankSum=1.01;QD=0.54;ReadPosRankSum=1.44;SOR=0.087	GT:AD:DP:GQ:PL	0/1:230,25:255:99:145,0,7351
-21	10141544	.	T	C	832.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.099e+00;ClippingRankSum=1.20;DP=236;ExcessHet=3.0103;FS=33.385;MLEAC=1;MLEAF=0.500;MQ=35.28;MQRankSum=0.575;QD=3.53;ReadPosRankSum=-4.560e-01;SOR=3.042	GT:AD:DP:GQ:PL	0/1:191,45:236:99:840,0,5870
-21	10141558	.	G	A	534.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.97;ClippingRankSum=0.721;DP=237;ExcessHet=3.0103;FS=15.079;MLEAC=1;MLEAF=0.500;MQ=35.93;MQRankSum=-1.527e+00;QD=2.27;ReadPosRankSum=-2.630e+00;SOR=1.989	GT:AD:DP:GQ:PL	0/1:202,34:236:99:542,0,6064
-21	10141613	.	G	C	1680.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.543e+00;ClippingRankSum=-1.172e+00;DP=182;ExcessHet=3.0103;FS=27.508;MLEAC=1;MLEAF=0.500;MQ=32.05;MQRankSum=3.08;QD=9.39;ReadPosRankSum=0.787;SOR=1.280	GT:AD:DP:GQ:PL	0/1:101,78:182:99:1688,0,2330
-21	10141635	.	T	A	51.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=0.266;DP=126;ExcessHet=3.0103;FS=28.772;MLEAC=1;MLEAF=0.500;MQ=29.99;MQRankSum=2.46;QD=0.41;ReadPosRankSum=-9.160e-01;SOR=4.802	GT:AD:DP:GQ:PGT:PID:PL	0/1:116,10:126:59:0|1:10141635_T_A:59,0,4756
-21	10141637	.	A	C	51.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.800e-02;ClippingRankSum=-5.900e-02;DP=122;ExcessHet=3.0103;FS=25.413;MLEAC=1;MLEAF=0.500;MQ=30.01;MQRankSum=2.36;QD=0.42;ReadPosRankSum=0.127;SOR=4.613	GT:AD:DP:GQ:PGT:PID:PL	0/1:113,9:122:59:0|1:10141635_T_A:59,0,4756
-21	10141799	.	A	AT	424.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.417e+00;ClippingRankSum=-5.060e-01;DP=132;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.91;MQRankSum=-1.173e+00;QD=4.04;ReadPosRankSum=-1.954e+00;SOR=0.619	GT:AD:DP:GQ:PL	0/1:80,25:107:99:432,0,1637
-21	10141819	.	G	A	308.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.79;ClippingRankSum=-1.373e+00;DP=103;ExcessHet=3.0103;FS=1.009;MLEAC=1;MLEAF=0.500;MQ=36.96;MQRankSum=-9.300e-02;QD=3.00;ReadPosRankSum=-7.330e-01;SOR=0.825	GT:AD:DP:GQ:PL	0/1:86,17:103:99:316,0,2749
-21	10141856	.	C	T	208.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.00;ClippingRankSum=-4.470e-01;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.96;MQRankSum=-8.620e-01;QD=3.79;ReadPosRankSum=1.60;SOR=0.725	GT:AD:DP:GQ:PL	0/1:45,10:55:99:216,0,1538
-21	10141857	.	G	A	438.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.38;ClippingRankSum=0.937;DP=54;ExcessHet=3.0103;FS=1.136;MLEAC=1;MLEAF=0.500;MQ=35.92;MQRankSum=-8.440e-01;QD=8.28;ReadPosRankSum=-1.085e+00;SOR=0.507	GT:AD:DP:GQ:PL	0/1:34,19:53:99:446,0,1050
-21	10142108	.	A	T	195.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.37;ClippingRankSum=-6.800e-02;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=-1.230e-01;QD=4.35;ReadPosRankSum=1.22;SOR=0.089	GT:AD:DP:GQ:PL	0/1:35,10:45:99:203,0,1018
-21	10143347	.	C	A	112.92	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.63;QD=22.58;SOR=1.981	GT:AD:DP:GQ:PL	1/1:0,5:5:15:127,15,0
-21	10143381	.	G	A	85.10	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.00;QD=21.27;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
-21	10143574	.	C	T	40.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.55;QD=20.14;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
-21	10143588	.	C	T	40.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.55;QD=20.14;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
-21	10143616	.	C	A	35.61	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DP=4;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=20.79;MQRankSum=0.736;QD=11.87;ReadPosRankSum=0.736;SOR=2.225	GT:AD:DP:GQ:PL	0/1:1,2:3:16:43,0,16
-21	10144135	.	T	C	56.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.14;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-21	10144149	.	C	T	78.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.17;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10144149_C_T:90,6,0
-21	10144152	.	A	C	78.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=26.80;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10144149_C_T:90,6,0
-21	10144183	.	C	T	56.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.14;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-21	10144319	.	C	T	136.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.660e-01;ClippingRankSum=-4.110e-01;DP=51;ExcessHet=3.0103;FS=7.498;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-3.660e-01;QD=2.68;ReadPosRankSum=-1.610e+00;SOR=0.716	GT:AD:DP:GQ:PL	0/1:39,12:51:99:144,0,811
-21	10144373	.	C	T	380.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.06;ClippingRankSum=-6.610e-01;DP=262;ExcessHet=3.0103;FS=1.246;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-1.207e+00;QD=1.45;ReadPosRankSum=2.15;SOR=0.811	GT:AD:DP:GQ:PL	0/1:214,48:262:99:388,0,4476
-21	10144601	.	C	CACACACACACAT	375.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220e-01;ClippingRankSum=0.933;DP=19;ExcessHet=3.0103;FS=18.921;MLEAC=1;MLEAF=0.500;MQ=28.25;MQRankSum=3.15;QD=20.87;ReadPosRankSum=1.38;SOR=3.226	GT:AD:DP:GQ:PL	0/1:8,10:18:99:383,0,292
-21	10144923	.	A	T	422.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.979;ClippingRankSum=1.50;DP=17;ExcessHet=3.0103;FS=2.869;MLEAC=1;MLEAF=0.500;MQ=33.15;MQRankSum=0.979;QD=28.17;ReadPosRankSum=0.979;SOR=0.097	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,11:15:99:0|1:10144923_A_T:430,0,287
-21	10144929	.	A	T	422.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=0.718;DP=17;ExcessHet=3.0103;FS=2.869;MLEAC=1;MLEAF=0.500;MQ=33.15;MQRankSum=0.849;QD=28.17;ReadPosRankSum=0.849;SOR=0.097	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,11:15:99:0|1:10144923_A_T:430,0,287
+21	10141275	.	G	A	823.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=-1.072e+00;DP=192;ExcessHet=3.0103;FS=2.122;MLEAC=1;MLEAF=0.500;MQ=39.97;MQRankSum=-6.555e+00;QD=4.29;ReadPosRankSum=1.45;SOR=0.896	GT:AD:DP:GQ:PL	0/1:144,48:192:99:831,0,4727
+21	10141304	.	C	A	3725.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.74;ClippingRankSum=-1.400e-01;DP=156;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=34.84;MQRankSum=-1.962e+00;QD=23.88;ReadPosRankSum=0.996;SOR=0.833	GT:AD:DP:GQ:PL	0/1:26,130:156:99:3733,0,508
+21	10141315	.	T	C	3693.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.661e+00;ClippingRankSum=-8.760e-01;DP=135;ExcessHet=3.0103;FS=3.354;MLEAC=1;MLEAF=0.500;MQ=33.43;MQRankSum=-1.395e+00;QD=27.36;ReadPosRankSum=-7.620e-01;SOR=0.381	GT:AD:DP:GQ:PL	0/1:19,116:135:99:3701,0,303
+21	10141318	.	C	G	719.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.240e-01;ClippingRankSum=0.129;DP=133;ExcessHet=3.0103;FS=9.719;MLEAC=1;MLEAF=0.500;MQ=33.35;MQRankSum=3.29;QD=5.41;ReadPosRankSum=8.000e-03;SOR=1.447	GT:AD:DP:GQ:PL	0/1:101,32:133:99:727,0,3058
+21	10141336	.	A	C	3056.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.600e-02;ClippingRankSum=0.317;DP=121;ExcessHet=3.0103;FS=7.047;MLEAC=1;MLEAF=0.500;MQ=32.61;MQRankSum=-9.140e-01;QD=25.26;ReadPosRankSum=-4.960e-01;SOR=0.922	GT:AD:DP:GQ:PL	0/1:17,104:121:99:3064,0,227
+21	10141374	.	T	C	2963.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;ClippingRankSum=-1.190e-01;DP=159;ExcessHet=3.0103;FS=21.794;MLEAC=1;MLEAF=0.500;MQ=34.24;MQRankSum=-2.720e-01;QD=18.64;ReadPosRankSum=0.031;SOR=1.204	GT:AD:DP:GQ:PL	0/1:53,106:159:99:2971,0,1606
+21	10141384	.	C	T	5509.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.12;ClippingRankSum=-2.630e-01;DP=168;ExcessHet=3.0103;FS=30.993;MLEAC=1;MLEAF=0.500;MQ=35.19;MQRankSum=1.20;QD=32.80;ReadPosRankSum=-2.050e-01;SOR=1.493	GT:AD:DP:GQ:PL	0/1:30,138:168:99:5517,0,585
+21	10141459	.	G	C	657.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.51;ClippingRankSum=-5.850e-01;DP=299;ExcessHet=3.0103;FS=18.034;MLEAC=1;MLEAF=0.500;MQ=31.64;MQRankSum=-4.960e-01;QD=2.21;ReadPosRankSum=1.14;SOR=2.629	GT:AD:DP:GQ:PL	0/1:257,40:297:99:665,0,8998
+21	10141464	.	C	G	589.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.044;ClippingRankSum=0.355;DP=298;ExcessHet=3.0103;FS=23.693;MLEAC=1;MLEAF=0.500;MQ=31.15;MQRankSum=-1.283e+00;QD=1.99;ReadPosRankSum=0.698;SOR=4.082	GT:AD:DP:GQ:PL	0/1:261,35:296:99:597,0,11007
+21	10141467	.	G	C	605.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.00;ClippingRankSum=0.044;DP=298;ExcessHet=3.0103;FS=35.719;MLEAC=1;MLEAF=0.500;MQ=31.13;MQRankSum=-2.625e+00;QD=2.17;ReadPosRankSum=1.40;SOR=4.804	GT:AD:DP:GQ:PL	0/1:246,33:296:99:613,0,10387
+21	10141513	.	A	T	137.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.520e-01;ClippingRankSum=0.373;DP=255;ExcessHet=3.0103;FS=17.023;MLEAC=1;MLEAF=0.500;MQ=34.23;MQRankSum=1.01;QD=0.54;ReadPosRankSum=1.44;SOR=0.087	GT:AD:DP:GQ:PL	0/1:230,25:255:99:145,0,7351
+21	10141544	.	T	C	832.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.099e+00;ClippingRankSum=1.20;DP=236;ExcessHet=3.0103;FS=33.385;MLEAC=1;MLEAF=0.500;MQ=35.28;MQRankSum=0.575;QD=3.53;ReadPosRankSum=-4.560e-01;SOR=3.042	GT:AD:DP:GQ:PL	0/1:191,45:236:99:840,0,5870
+21	10141558	.	G	A	534.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.97;ClippingRankSum=0.721;DP=237;ExcessHet=3.0103;FS=15.079;MLEAC=1;MLEAF=0.500;MQ=35.93;MQRankSum=-1.527e+00;QD=2.27;ReadPosRankSum=-2.630e+00;SOR=1.989	GT:AD:DP:GQ:PL	0/1:202,34:236:99:542,0,6064
+21	10141613	.	G	C	1680.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.543e+00;ClippingRankSum=-1.172e+00;DP=182;ExcessHet=3.0103;FS=27.508;MLEAC=1;MLEAF=0.500;MQ=32.05;MQRankSum=3.08;QD=9.39;ReadPosRankSum=0.787;SOR=1.280	GT:AD:DP:GQ:PL	0/1:101,78:182:99:1688,0,2330
+21	10141635	.	T	A	51.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=0.266;DP=126;ExcessHet=3.0103;FS=28.772;MLEAC=1;MLEAF=0.500;MQ=29.99;MQRankSum=2.46;QD=0.41;ReadPosRankSum=-9.160e-01;SOR=4.802	GT:AD:DP:GQ:PGT:PID:PL	0/1:116,10:126:59:0|1:10141635_T_A:59,0,4756
+21	10141637	.	A	C	51.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.800e-02;ClippingRankSum=-5.900e-02;DP=122;ExcessHet=3.0103;FS=25.413;MLEAC=1;MLEAF=0.500;MQ=30.01;MQRankSum=2.36;QD=0.42;ReadPosRankSum=0.127;SOR=4.613	GT:AD:DP:GQ:PGT:PID:PL	0/1:113,9:122:59:0|1:10141635_T_A:59,0,4756
+21	10141799	.	A	AT	424.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.417e+00;ClippingRankSum=-5.060e-01;DP=132;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.91;MQRankSum=-1.173e+00;QD=4.04;ReadPosRankSum=-1.954e+00;SOR=0.619	GT:AD:DP:GQ:PL	0/1:80,25:107:99:432,0,1637
+21	10141819	.	G	A	308.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.79;ClippingRankSum=-1.373e+00;DP=103;ExcessHet=3.0103;FS=1.009;MLEAC=1;MLEAF=0.500;MQ=36.96;MQRankSum=-9.300e-02;QD=3.00;ReadPosRankSum=-7.330e-01;SOR=0.825	GT:AD:DP:GQ:PL	0/1:86,17:103:99:316,0,2749
+21	10141856	.	C	T	208.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.00;ClippingRankSum=-4.470e-01;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.96;MQRankSum=-8.620e-01;QD=3.79;ReadPosRankSum=1.60;SOR=0.725	GT:AD:DP:GQ:PL	0/1:45,10:55:99:216,0,1538
+21	10141857	.	G	A	438.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.38;ClippingRankSum=0.937;DP=54;ExcessHet=3.0103;FS=1.136;MLEAC=1;MLEAF=0.500;MQ=35.92;MQRankSum=-8.440e-01;QD=8.28;ReadPosRankSum=-1.085e+00;SOR=0.507	GT:AD:DP:GQ:PL	0/1:34,19:53:99:446,0,1050
+21	10142108	.	A	T	195.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.37;ClippingRankSum=-6.800e-02;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=-1.230e-01;QD=4.35;ReadPosRankSum=1.22;SOR=0.089	GT:AD:DP:GQ:PL	0/1:35,10:45:99:203,0,1018
+21	10143347	.	C	A	112.96	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.63;QD=22.59;SOR=1.981	GT:AD:DP:GQ:PL	1/1:0,5:5:15:127,15,0
+21	10143381	.	G	A	85.14	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.00;QD=21.29;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,4:4:12:99,12,0
+21	10143574	.	C	T	40.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.55;QD=20.16;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
+21	10143588	.	C	T	40.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.55;QD=20.16;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:52,6,0
+21	10143616	.	C	A	35.65	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DP=4;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=20.79;MQRankSum=0.736;QD=11.88;ReadPosRankSum=0.736;SOR=2.225	GT:AD:DP:GQ:PL	0/1:1,2:3:16:43,0,16
+21	10144135	.	T	C	56.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.16;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
+21	10144149	.	C	T	78.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.17;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10144149_C_T:90,6,0
+21	10144152	.	A	C	78.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=26.80;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10144149_C_T:90,6,0
+21	10144183	.	C	T	56.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=28.16;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
+21	10144319	.	C	T	136.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.660e-01;ClippingRankSum=-4.110e-01;DP=51;ExcessHet=3.0103;FS=7.498;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-3.660e-01;QD=2.68;ReadPosRankSum=-1.610e+00;SOR=0.716	GT:AD:DP:GQ:PL	0/1:39,12:51:99:144,0,811
+21	10144373	.	C	T	380.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.06;ClippingRankSum=-6.610e-01;DP=262;ExcessHet=3.0103;FS=1.246;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-1.207e+00;QD=1.45;ReadPosRankSum=2.15;SOR=0.811	GT:AD:DP:GQ:PL	0/1:214,48:262:99:388,0,4476
+21	10144601	.	C	CACACACACACAT	375.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220e-01;ClippingRankSum=0.933;DP=19;ExcessHet=3.0103;FS=18.921;MLEAC=1;MLEAF=0.500;MQ=28.25;MQRankSum=3.15;QD=20.87;ReadPosRankSum=1.38;SOR=3.226	GT:AD:DP:GQ:PL	0/1:8,10:18:99:383,0,292
+21	10144923	.	A	T	422.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.979;ClippingRankSum=1.50;DP=17;ExcessHet=3.0103;FS=2.869;MLEAC=1;MLEAF=0.500;MQ=33.15;MQRankSum=0.979;QD=28.18;ReadPosRankSum=0.979;SOR=0.097	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,11:15:99:0|1:10144923_A_T:430,0,287
+21	10144929	.	A	T	422.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.15;ClippingRankSum=0.718;DP=17;ExcessHet=3.0103;FS=2.869;MLEAC=1;MLEAF=0.500;MQ=33.15;MQRankSum=0.849;QD=28.18;ReadPosRankSum=0.849;SOR=0.097	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,11:15:99:0|1:10144923_A_T:430,0,287
 21	10144947	.	TTA	T	422.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;ClippingRankSum=0.495;DP=16;ExcessHet=3.0103;FS=6.008;MLEAC=1;MLEAF=0.500;MQ=33.39;MQRankSum=1.06;QD=30.19;ReadPosRankSum=-3.540e-01;SOR=0.075	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,10:14:99:0|1:10144923_A_T:430,0,287
-21	10146228	.	A	T	812.03	.	AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.73;QD=26.00;SOR=1.508	GT:AD:DP:GQ:PL	1/1:0,21:21:63:826,63,0
+21	10146228	.	A	T	812.06	.	AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.73;QD=26.00;SOR=1.508	GT:AD:DP:GQ:PL	1/1:0,21:21:63:826,63,0
 21	10148552	.	CTT	C	537.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.02;ClippingRankSum=-1.168e+00;DP=118;ExcessHet=3.0103;FS=21.908;MLEAC=1;MLEAF=0.500;MQ=26.22;MQRankSum=-4.914e+00;QD=4.59;ReadPosRankSum=-3.100e-01;SOR=4.171	GT:AD:DP:GQ:PL	0/1:95,22:117:99:545,0,3351
-21	10148558	.	T	C	194.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.471e+00;ClippingRankSum=-6.900e-02;DP=120;ExcessHet=3.0103;FS=4.050;MLEAC=1;MLEAF=0.500;MQ=26.44;MQRankSum=-1.730e-01;QD=1.62;ReadPosRankSum=1.32;SOR=0.307	GT:AD:DP:GQ:PL	0/1:99,21:120:99:202,0,2971
-21	10148867	.	A	T	96.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.58;ClippingRankSum=-1.661e+00;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.38;MQRankSum=-2.382e+00;QD=2.54;ReadPosRankSum=0.901;SOR=0.044	GT:AD:DP:GQ:PL	0/1:32,6:38:99:104,0,889
-21	10148902	.	A	C	128.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.586e+00;ClippingRankSum=-2.740e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.28;MQRankSum=-2.952e+00;QD=4.95;ReadPosRankSum=0.091;SOR=0.105	GT:AD:DP:GQ:PL	0/1:20,6:26:99:136,0,583
-21	10150460	.	A	C	71.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=25.04;MQRankSum=0.358;QD=14.32;ReadPosRankSum=-3.580e-01;SOR=2.833	GT:AD:DP:GQ:PL	0/1:2,3:5:38:79,0,38
-21	10150497	.	C	A	193.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.684;DP=9;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=23.73;MQRankSum=-1.517e+00;QD=24.20;ReadPosRankSum=-1.920e+00;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	0/1:3,5:8:99:0|1:10150497_C_A:201,0,111
-21	10150507	.	G	A	190.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.88;ClippingRankSum=0.361;DP=10;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=23.57;MQRankSum=0.729;QD=21.18;ReadPosRankSum=0.729;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,5:9:99:0|1:10150497_C_A:198,0,135
-21	10150746	.	A	G	287.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.016e+00;ClippingRankSum=0.660;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.36;MQRankSum=-1.369e+00;QD=22.12;ReadPosRankSum=-1.093e+00;SOR=0.446	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10150746_A_G:295,0,295
-21	10150752	.	C	T	346.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.75;ClippingRankSum=-1.540e-01;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.54;MQRankSum=-3.100e-02;QD=15.07;ReadPosRankSum=-3.100e-02;SOR=0.569	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,11:23:99:0|1:10150746_A_G:354,0,415
-21	10150817	.	C	T	1263.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.632;ClippingRankSum=0.458;DP=96;ExcessHet=3.0103;FS=3.951;MLEAC=1;MLEAF=0.500;MQ=22.32;MQRankSum=-1.101e+00;QD=13.16;ReadPosRankSum=0.670;SOR=1.109	GT:AD:DP:GQ:PL	0/1:36,60:96:99:1271,0,700
-21	10150942	.	C	T	2540.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.74;ClippingRankSum=-4.630e-01;DP=215;ExcessHet=3.0103;FS=10.872;MLEAC=1;MLEAF=0.500;MQ=20.29;MQRankSum=2.80;QD=11.82;ReadPosRankSum=-3.647e+00;SOR=1.020	GT:AD:DP:GQ:PL	0/1:144,71:215:99:2548,0,5822
-21	10150946	.	A	T	1855.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.129e+00;ClippingRankSum=-2.130e-01;DP=215;ExcessHet=3.0103;FS=10.872;MLEAC=1;MLEAF=0.500;MQ=20.29;MQRankSum=2.35;QD=9.87;ReadPosRankSum=-4.078e+00;SOR=1.020	GT:AD:DP:GQ:PL	0/1:144,44:215:99:1863,0,5823
-21	10150979	.	G	A	148.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.440;ClippingRankSum=-6.490e-01;DP=155;ExcessHet=3.0103;FS=2.918;MLEAC=1;MLEAF=0.500;MQ=20.04;MQRankSum=0.640;QD=0.96;ReadPosRankSum=-1.870e-01;SOR=0.552	GT:AD:DP:GQ:PL	0/1:130,25:155:99:156,0,3086
-21	10151080	.	T	A	51.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-01;ClippingRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=0.00;QD=7.37;ReadPosRankSum=0.550;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:59:59,0,84
-21	10152244	.	C	T	1102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.40;ClippingRankSum=-1.010e-01;DP=421;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.37;MQRankSum=-2.110e-01;QD=2.62;ReadPosRankSum=3.45;SOR=0.660	GT:AD:DP:GQ:PL	0/1:327,94:421:99:1110,0,8207
-21	10152254	.	C	A	258.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.78;ClippingRankSum=-4.440e-01;DP=465;ExcessHet=3.0103;FS=5.240;MLEAC=1;MLEAF=0.500;MQ=20.34;MQRankSum=-6.500e-02;QD=0.56;ReadPosRankSum=-8.010e-01;SOR=0.736	GT:AD:DP:GQ:PL	0/1:397,67:464:99:266,0,10381
-21	10152554	.	A	G	63.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.48;MQRankSum=-9.880e-01;QD=10.60;ReadPosRankSum=0.406;SOR=0.693	GT:AD:DP:GQ:PL	0/1:3,3:6:71:71,0,72
-21	10152578	.	A	G	71.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.537e+00;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.48;MQRankSum=0.406;QD=11.93;ReadPosRankSum=1.54;SOR=0.693	GT:AD:DP:GQ:PL	0/1:3,3:6:71:79,0,71
-21	10152683	.	G	C	88.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.64;MQRankSum=0.406;QD=14.77;ReadPosRankSum=0.988;SOR=2.093	GT:AD:DP:GQ:PL	0/1:3,3:6:73:96,0,73
-21	10152722	.	T	C	384.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.433e+00;ClippingRankSum=1.28;DP=36;ExcessHet=3.0103;FS=10.571;MLEAC=1;MLEAF=0.500;MQ=23.98;MQRankSum=-9.020e-01;QD=10.68;ReadPosRankSum=1.41;SOR=3.198	GT:AD:DP:GQ:PL	0/1:18,18:36:99:392,0,388
-21	10152752	.	C	A	367.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.61;ClippingRankSum=0.394;DP=46;ExcessHet=3.0103;FS=18.165;MLEAC=1;MLEAF=0.500;MQ=23.56;MQRankSum=-6.640e-01;QD=7.99;ReadPosRankSum=1.27;SOR=3.611	GT:AD:DP:GQ:PL	0/1:28,18:46:99:375,0,585
-21	10152991	.	A	T	98.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.750e-01;ClippingRankSum=0.344;DP=80;ExcessHet=3.0103;FS=7.117;MLEAC=1;MLEAF=0.500;MQ=25.08;MQRankSum=0.559;QD=1.23;ReadPosRankSum=0.330;SOR=1.942	GT:AD:DP:GQ:PL	0/1:68,12:80:99:106,0,1911
+21	10148558	.	T	C	194.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.471e+00;ClippingRankSum=-6.900e-02;DP=120;ExcessHet=3.0103;FS=4.050;MLEAC=1;MLEAF=0.500;MQ=26.44;MQRankSum=-1.730e-01;QD=1.62;ReadPosRankSum=1.32;SOR=0.307	GT:AD:DP:GQ:PL	0/1:99,21:120:99:202,0,2971
+21	10148867	.	A	T	96.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.58;ClippingRankSum=-1.661e+00;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.38;MQRankSum=-2.382e+00;QD=2.54;ReadPosRankSum=0.901;SOR=0.044	GT:AD:DP:GQ:PL	0/1:32,6:38:99:104,0,889
+21	10148902	.	A	C	128.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.586e+00;ClippingRankSum=-2.740e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.28;MQRankSum=-2.952e+00;QD=4.95;ReadPosRankSum=0.091;SOR=0.105	GT:AD:DP:GQ:PL	0/1:20,6:26:99:136,0,583
+21	10150460	.	A	C	71.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=25.04;MQRankSum=0.358;QD=14.33;ReadPosRankSum=-3.580e-01;SOR=2.833	GT:AD:DP:GQ:PL	0/1:2,3:5:38:79,0,38
+21	10150497	.	C	A	193.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.684;DP=9;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=23.73;MQRankSum=-1.517e+00;QD=24.20;ReadPosRankSum=-1.920e+00;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	0/1:3,5:8:99:0|1:10150497_C_A:201,0,111
+21	10150507	.	G	A	190.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.88;ClippingRankSum=0.361;DP=10;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=23.57;MQRankSum=0.729;QD=21.18;ReadPosRankSum=0.729;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,5:9:99:0|1:10150497_C_A:198,0,135
+21	10150746	.	A	G	287.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.016e+00;ClippingRankSum=0.660;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.36;MQRankSum=-1.369e+00;QD=22.13;ReadPosRankSum=-1.093e+00;SOR=0.446	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10150746_A_G:295,0,295
+21	10150752	.	C	T	346.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.75;ClippingRankSum=-1.540e-01;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.54;MQRankSum=-3.100e-02;QD=15.07;ReadPosRankSum=-3.100e-02;SOR=0.569	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,11:23:99:0|1:10150746_A_G:354,0,415
+21	10150817	.	C	T	1263.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.632;ClippingRankSum=0.458;DP=96;ExcessHet=3.0103;FS=3.951;MLEAC=1;MLEAF=0.500;MQ=22.32;MQRankSum=-1.101e+00;QD=13.16;ReadPosRankSum=0.670;SOR=1.109	GT:AD:DP:GQ:PL	0/1:36,60:96:99:1271,0,700
+21	10150942	.	C	T	2540.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.74;ClippingRankSum=-4.630e-01;DP=215;ExcessHet=3.0103;FS=10.872;MLEAC=1;MLEAF=0.500;MQ=20.29;MQRankSum=2.80;QD=11.82;ReadPosRankSum=-3.647e+00;SOR=1.020	GT:AD:DP:GQ:PL	0/1:144,71:215:99:2548,0,5822
+21	10150946	.	A	T	1855.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.129e+00;ClippingRankSum=-2.130e-01;DP=215;ExcessHet=3.0103;FS=10.872;MLEAC=1;MLEAF=0.500;MQ=20.29;MQRankSum=2.35;QD=9.87;ReadPosRankSum=-4.078e+00;SOR=1.020	GT:AD:DP:GQ:PL	0/1:144,44:215:99:1863,0,5823
+21	10150979	.	G	A	148.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.440;ClippingRankSum=-6.490e-01;DP=155;ExcessHet=3.0103;FS=2.918;MLEAC=1;MLEAF=0.500;MQ=20.04;MQRankSum=0.640;QD=0.96;ReadPosRankSum=-1.870e-01;SOR=0.552	GT:AD:DP:GQ:PL	0/1:130,25:155:99:156,0,3086
+21	10151080	.	T	A	51.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-01;ClippingRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=0.00;QD=7.38;ReadPosRankSum=0.550;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:59:59,0,84
+21	10152244	.	C	T	1102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.40;ClippingRankSum=-1.010e-01;DP=421;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.37;MQRankSum=-2.110e-01;QD=2.62;ReadPosRankSum=3.45;SOR=0.660	GT:AD:DP:GQ:PL	0/1:327,94:421:99:1110,0,8207
+21	10152254	.	C	A	258.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.78;ClippingRankSum=-4.440e-01;DP=465;ExcessHet=3.0103;FS=5.240;MLEAC=1;MLEAF=0.500;MQ=20.34;MQRankSum=-6.500e-02;QD=0.56;ReadPosRankSum=-8.010e-01;SOR=0.736	GT:AD:DP:GQ:PL	0/1:397,67:464:99:266,0,10381
+21	10152554	.	A	G	63.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.48;MQRankSum=-9.880e-01;QD=10.61;ReadPosRankSum=0.406;SOR=0.693	GT:AD:DP:GQ:PL	0/1:3,3:6:71:71,0,72
+21	10152578	.	A	G	71.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.537e+00;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.48;MQRankSum=0.406;QD=11.94;ReadPosRankSum=1.54;SOR=0.693	GT:AD:DP:GQ:PL	0/1:3,3:6:71:79,0,71
+21	10152683	.	G	C	88.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.64;MQRankSum=0.406;QD=14.77;ReadPosRankSum=0.988;SOR=2.093	GT:AD:DP:GQ:PL	0/1:3,3:6:73:96,0,73
+21	10152722	.	T	C	384.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.433e+00;ClippingRankSum=1.28;DP=36;ExcessHet=3.0103;FS=10.571;MLEAC=1;MLEAF=0.500;MQ=23.98;MQRankSum=-9.020e-01;QD=10.68;ReadPosRankSum=1.41;SOR=3.198	GT:AD:DP:GQ:PL	0/1:18,18:36:99:392,0,388
+21	10152752	.	C	A	367.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.61;ClippingRankSum=0.394;DP=46;ExcessHet=3.0103;FS=18.165;MLEAC=1;MLEAF=0.500;MQ=23.56;MQRankSum=-6.640e-01;QD=7.99;ReadPosRankSum=1.27;SOR=3.611	GT:AD:DP:GQ:PL	0/1:28,18:46:99:375,0,585
+21	10152991	.	A	T	98.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.750e-01;ClippingRankSum=0.344;DP=80;ExcessHet=3.0103;FS=7.117;MLEAC=1;MLEAF=0.500;MQ=25.08;MQRankSum=0.559;QD=1.23;ReadPosRankSum=0.330;SOR=1.942	GT:AD:DP:GQ:PL	0/1:68,12:80:99:106,0,1911
 21	10153005	.	CA	C	148.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-02;ClippingRankSum=0.493;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.14;MQRankSum=-2.414e+00;QD=1.91;ReadPosRankSum=0.590;SOR=0.545	GT:AD:DP:GQ:PL	0/1:69,9:83:99:156,0,2946
-21	10153012	.	A	T	147.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.267e+00;ClippingRankSum=0.124;DP=83;ExcessHet=3.0103;FS=1.481;MLEAC=1;MLEAF=0.500;MQ=25.14;MQRankSum=-1.574e+00;QD=1.78;ReadPosRankSum=-6.960e-01;SOR=1.150	GT:AD:DP:GQ:PL	0/1:74,9:83:99:155,0,3080
-21	10156598	.	T	C	35.44	.	AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.00;QD=30.02;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,1:1:3:1|1:10156598_T_C:45,3,0
-21	10156608	.	C	T	35.44	.	AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.00;QD=31.98;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,1:1:3:1|1:10156598_T_C:45,3,0
-21	10156615	.	T	C	78.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.32;QD=27.51;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10156598_T_C:90,6,0
-21	10156619	.	T	G	77.94	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.31;QD=29.11;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:5:1|1:10156598_T_C:89,5,0
-21	10156620	.	T	C	77.94	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.31;QD=28.08;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:5:1|1:10156598_T_C:89,5,0
-21	10156680	.	C	T	87.80	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.83;QD=29.27;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:101,9,0
-21	10156883	.	A	G	171.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.000e-02;ClippingRankSum=0.370;DP=55;ExcessHet=3.0103;FS=7.135;MLEAC=1;MLEAF=0.500;MQ=21.82;MQRankSum=4.48;QD=3.12;ReadPosRankSum=0.871;SOR=0.100	GT:AD:DP:GQ:PGT:PID:PL	0/1:47,8:55:99:0|1:10156883_A_G:179,0,2999
-21	10156886	.	G	A	156.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=1.69;DP=62;ExcessHet=3.0103;FS=7.023;MLEAC=1;MLEAF=0.500;MQ=21.62;MQRankSum=4.53;QD=2.53;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,8:62:99:0|1:10156883_A_G:164,0,3322
-21	10156896	.	G	A	87.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.27;ClippingRankSum=-3.250e-01;DP=81;ExcessHet=3.0103;FS=6.689;MLEAC=1;MLEAF=0.500;MQ=21.25;MQRankSum=4.61;QD=1.08;ReadPosRankSum=2.22;SOR=0.124	GT:AD:DP:GQ:PGT:PID:PL	0/1:73,8:81:95:0|1:10156883_A_G:95,0,4706
+21	10153012	.	A	T	147.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.267e+00;ClippingRankSum=0.124;DP=83;ExcessHet=3.0103;FS=1.481;MLEAC=1;MLEAF=0.500;MQ=25.14;MQRankSum=-1.574e+00;QD=1.78;ReadPosRankSum=-6.960e-01;SOR=1.150	GT:AD:DP:GQ:PL	0/1:74,9:83:99:155,0,3080
+21	10156598	.	T	C	35.48	.	AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.00;QD=30.02;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,1:1:3:1|1:10156598_T_C:45,3,0
+21	10156608	.	C	T	35.48	.	AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.00;QD=31.98;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,1:1:3:1|1:10156598_T_C:45,3,0
+21	10156615	.	T	C	78.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.32;QD=27.51;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10156598_T_C:90,6,0
+21	10156619	.	T	G	77.98	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.31;QD=29.11;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:5:1|1:10156598_T_C:89,5,0
+21	10156620	.	T	C	77.98	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.31;QD=28.08;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:5:1|1:10156598_T_C:89,5,0
+21	10156680	.	C	T	87.84	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.83;QD=29.28;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:101,9,0
+21	10156883	.	A	G	171.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.000e-02;ClippingRankSum=0.370;DP=55;ExcessHet=3.0103;FS=7.135;MLEAC=1;MLEAF=0.500;MQ=21.82;MQRankSum=4.48;QD=3.12;ReadPosRankSum=0.871;SOR=0.100	GT:AD:DP:GQ:PGT:PID:PL	0/1:47,8:55:99:0|1:10156883_A_G:179,0,2999
+21	10156886	.	G	A	156.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=1.69;DP=62;ExcessHet=3.0103;FS=7.023;MLEAC=1;MLEAF=0.500;MQ=21.62;MQRankSum=4.53;QD=2.53;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,8:62:99:0|1:10156883_A_G:164,0,3322
+21	10156896	.	G	A	87.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.27;ClippingRankSum=-3.250e-01;DP=81;ExcessHet=3.0103;FS=6.689;MLEAC=1;MLEAF=0.500;MQ=21.25;MQRankSum=4.61;QD=1.08;ReadPosRankSum=2.22;SOR=0.124	GT:AD:DP:GQ:PGT:PID:PL	0/1:73,8:81:95:0|1:10156883_A_G:95,0,4706
 21	10156898	.	GC	G	75.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.24;ClippingRankSum=-1.038e+00;DP=88;ExcessHet=3.0103;FS=6.652;MLEAC=1;MLEAF=0.500;MQ=21.16;MQRankSum=4.64;QD=0.86;ReadPosRankSum=2.45;SOR=0.126	GT:AD:DP:GQ:PGT:PID:PL	0/1:80,8:88:83:0|1:10156883_A_G:83,0,4793
-21	10156902	.	A	T	69.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.81;ClippingRankSum=1.10;DP=94;ExcessHet=3.0103;FS=6.564;MLEAC=1;MLEAF=0.500;MQ=21.08;MQRankSum=4.65;QD=0.74;ReadPosRankSum=2.63;SOR=0.132	GT:AD:DP:GQ:PGT:PID:PL	0/1:86,8:94:77:0|1:10156883_A_G:77,0,4837
-21	10156953	.	G	T	212.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.92;ClippingRankSum=0.172;DP=108;ExcessHet=3.0103;FS=6.992;MLEAC=1;MLEAF=0.500;MQ=20.75;MQRankSum=-3.322e+00;QD=1.97;ReadPosRankSum=-5.760e-01;SOR=1.582	GT:AD:DP:GQ:PL	0/1:86,22:108:99:220,0,1852
-21	10157182	.	G	A	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.250e-01;ClippingRankSum=0.255;DP=15;ExcessHet=3.0103;FS=10.212;MLEAC=1;MLEAF=0.500;MQ=21.42;MQRankSum=2.12;QD=2.51;ReadPosRankSum=0.934;SOR=2.212	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10157182_G_A:45,0,540
-21	10157183	.	G	A	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.340e-01;ClippingRankSum=1.27;DP=15;ExcessHet=3.0103;FS=10.212;MLEAC=1;MLEAF=0.500;MQ=21.42;MQRankSum=2.12;QD=2.51;ReadPosRankSum=1.27;SOR=2.212	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10157182_G_A:45,0,540
-21	10157194	.	A	C	52.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.980e-01;ClippingRankSum=1.73;DP=10;ExcessHet=3.0103;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=22.10;MQRankSum=1.73;QD=5.26;ReadPosRankSum=1.73;SOR=2.217	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,2:10:60:0|1:10157194_A_C:60,0,330
-21	10157197	.	G	C	52.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;ClippingRankSum=0.898;DP=10;ExcessHet=3.0103;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=22.10;MQRankSum=1.73;QD=5.26;ReadPosRankSum=1.73;SOR=2.217	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,2:10:60:0|1:10157194_A_C:60,0,330
-21	10157211	.	A	T	48.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.91;MQRankSum=1.03;QD=12.15;ReadPosRankSum=1.03;SOR=2.303	GT:AD:DP:GQ:PL	0/1:2,2:4:37:56,0,37
-21	10157236	.	T	G	78.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=23.23;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10157236_T_G:90,6,0
-21	10157242	.	G	A	78.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=29.03;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10157236_T_G:90,6,0
-21	10158602	.	C	T	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;ClippingRankSum=-4.200e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.67;MQRankSum=-1.800e+00;QD=2.41;ReadPosRankSum=-9.000e-01;SOR=0.061	GT:AD:DP:GQ:PL	0/1:23,5:28:75:75,0,730
-21	10158677	.	C	T	70.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.81;ClippingRankSum=0.107;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.16;MQRankSum=1.39;QD=2.72;ReadPosRankSum=1.03;SOR=0.046	GT:AD:DP:GQ:PL	0/1:22,4:26:78:78,0,717
-21	10158704	.	A	C	61.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083e+00;ClippingRankSum=0.217;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.86;MQRankSum=0.794;QD=4.11;ReadPosRankSum=0.361;SOR=0.090	GT:AD:DP:GQ:PL	0/1:12,3:15:69:69,0,364
-21	10158906	.	C	T	193.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.11;ClippingRankSum=-1.079e+00;DP=61;ExcessHet=3.0103;FS=1.578;MLEAC=1;MLEAF=0.500;MQ=35.92;MQRankSum=0.545;QD=3.17;ReadPosRankSum=-2.670e-01;SOR=0.372	GT:AD:DP:GQ:PGT:PID:PL	0/1:53,8:61:99:0|1:10158906_C_T:201,0,3772
-21	10158913	.	C	G	160.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.383e+00;ClippingRankSum=0.367;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.03;MQRankSum=1.41;QD=2.14;ReadPosRankSum=0.236;SOR=0.588	GT:AD:DP:GQ:PGT:PID:PL	0/1:66,9:75:99:0|1:10158906_C_T:168,0,4155
-21	10159130	.	G	C	154.92	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=30.98;SOR=3.611	GT:AD:DP:GQ:PL	1/1:0,5:5:15:169,15,0
-21	10159246	.	G	A	245.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.82;ClippingRankSum=-4.190e-01;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.15;MQRankSum=-1.709e+00;QD=3.72;ReadPosRankSum=1.02;SOR=0.065	GT:AD:DP:GQ:PL	0/1:53,13:66:99:253,0,1774
-21	10159282	.	A	G	393.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974e+00;ClippingRankSum=1.44;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=-1.733e+00;QD=7.16;ReadPosRankSum=0.158;SOR=0.166	GT:AD:DP:GQ:PL	0/1:39,16:55:99:401,0,1305
-21	10159336	.	G	A	73.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.34;ClippingRankSum=0.467;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.35;MQRankSum=-1.246e+00;QD=5.26;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:11,3:14:81:0|1:10159314_A_G:81,0,704
-21	10159341	.	G	T	94.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;ClippingRankSum=0.296;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.49;MQRankSum=-7.310e-01;QD=9.46;ReadPosRankSum=0.731;SOR=0.223	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,3:10:99:0|1:10159314_A_G:102,0,397
-21	10160074	.	A	G	638.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.096e+00;ClippingRankSum=-6.190e-01;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.85;MQRankSum=-7.840e-01;QD=30.41;ReadPosRankSum=1.69;SOR=2.200	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,16:21:99:0|1:10160056_A_C:646,0,174
-21	10160084	.	G	A	365.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.29;ClippingRankSum=0.578;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.86;MQRankSum=0.578;QD=20.31;ReadPosRankSum=1.38;SOR=0.914	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,10:18:99:0|1:10160056_A_C:373,0,400
-21	10160095	.	T	C	158.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.360e-01;ClippingRankSum=0.071;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.10;MQRankSum=-1.768e+00;QD=11.33;ReadPosRankSum=-1.202e+00;SOR=0.188	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,4:14:99:0|1:10160056_A_C:166,0,481
-21	10160106	.	C	T	262.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.66;ClippingRankSum=-2.780e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.39;MQRankSum=0.597;QD=23.87;ReadPosRankSum=-5.970e-01;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,7:11:99:0|1:10160056_A_C:270,0,207
-21	10160281	.	C	G	58.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.720e-01;ClippingRankSum=0.057;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.85;MQRankSum=1.83;QD=1.63;ReadPosRankSum=-9.160e-01;SOR=0.580	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,3:36:66:0|1:10160281_C_G:66,0,1416
-21	10160292	.	A	T	94.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;ClippingRankSum=1.27;DP=43;ExcessHet=3.0103;FS=2.071;MLEAC=1;MLEAF=0.500;MQ=28.19;MQRankSum=1.44;QD=2.20;ReadPosRankSum=0.732;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,4:43:99:0|1:10160281_C_G:102,0,1620
-21	10160293	.	A	T	95.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.677e+00;ClippingRankSum=-8.160e-01;DP=45;ExcessHet=3.0103;FS=6.287;MLEAC=1;MLEAF=0.500;MQ=28.02;MQRankSum=1.97;QD=2.22;ReadPosRankSum=-1.173e+00;SOR=0.941	GT:AD:DP:GQ:PL	0/1:37,6:45:99:103,0,1553
+21	10156902	.	A	T	69.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.81;ClippingRankSum=1.10;DP=94;ExcessHet=3.0103;FS=6.564;MLEAC=1;MLEAF=0.500;MQ=21.08;MQRankSum=4.65;QD=0.74;ReadPosRankSum=2.63;SOR=0.132	GT:AD:DP:GQ:PGT:PID:PL	0/1:86,8:94:77:0|1:10156883_A_G:77,0,4837
+21	10156953	.	G	T	212.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.92;ClippingRankSum=0.172;DP=108;ExcessHet=3.0103;FS=6.992;MLEAC=1;MLEAF=0.500;MQ=20.75;MQRankSum=-3.322e+00;QD=1.97;ReadPosRankSum=-5.760e-01;SOR=1.582	GT:AD:DP:GQ:PL	0/1:86,22:108:99:220,0,1852
+21	10157182	.	G	A	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.250e-01;ClippingRankSum=0.255;DP=15;ExcessHet=3.0103;FS=10.212;MLEAC=1;MLEAF=0.500;MQ=21.42;MQRankSum=2.12;QD=2.51;ReadPosRankSum=0.934;SOR=2.212	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10157182_G_A:45,0,540
+21	10157183	.	G	A	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.340e-01;ClippingRankSum=1.27;DP=15;ExcessHet=3.0103;FS=10.212;MLEAC=1;MLEAF=0.500;MQ=21.42;MQRankSum=2.12;QD=2.51;ReadPosRankSum=1.27;SOR=2.212	GT:AD:DP:GQ:PGT:PID:PL	0/1:13,2:15:45:0|1:10157182_G_A:45,0,540
+21	10157194	.	A	C	52.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.980e-01;ClippingRankSum=1.73;DP=10;ExcessHet=3.0103;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=22.10;MQRankSum=1.73;QD=5.26;ReadPosRankSum=1.73;SOR=2.217	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,2:10:60:0|1:10157194_A_C:60,0,330
+21	10157197	.	G	C	52.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;ClippingRankSum=0.898;DP=10;ExcessHet=3.0103;FS=8.751;MLEAC=1;MLEAF=0.500;MQ=22.10;MQRankSum=1.73;QD=5.26;ReadPosRankSum=1.73;SOR=2.217	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,2:10:60:0|1:10157194_A_C:60,0,330
+21	10157211	.	A	T	48.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=-1.026e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.91;MQRankSum=1.03;QD=12.16;ReadPosRankSum=1.03;SOR=2.303	GT:AD:DP:GQ:PL	0/1:2,2:4:37:56,0,37
+21	10157236	.	T	G	78.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=23.23;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10157236_T_G:90,6,0
+21	10157242	.	G	A	78.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;QD=29.03;SOR=2.303	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10157236_T_G:90,6,0
+21	10158602	.	C	T	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;ClippingRankSum=-4.200e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.67;MQRankSum=-1.800e+00;QD=2.42;ReadPosRankSum=-9.000e-01;SOR=0.061	GT:AD:DP:GQ:PL	0/1:23,5:28:75:75,0,730
+21	10158677	.	C	T	70.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.81;ClippingRankSum=0.107;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.16;MQRankSum=1.39;QD=2.72;ReadPosRankSum=1.03;SOR=0.046	GT:AD:DP:GQ:PL	0/1:22,4:26:78:78,0,717
+21	10158704	.	A	C	61.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083e+00;ClippingRankSum=0.217;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.86;MQRankSum=0.794;QD=4.11;ReadPosRankSum=0.361;SOR=0.090	GT:AD:DP:GQ:PL	0/1:12,3:15:69:69,0,364
+21	10158906	.	C	T	193.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.11;ClippingRankSum=-1.079e+00;DP=61;ExcessHet=3.0103;FS=1.578;MLEAC=1;MLEAF=0.500;MQ=35.92;MQRankSum=0.545;QD=3.17;ReadPosRankSum=-2.670e-01;SOR=0.372	GT:AD:DP:GQ:PGT:PID:PL	0/1:53,8:61:99:0|1:10158906_C_T:201,0,3772
+21	10158913	.	C	G	160.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.383e+00;ClippingRankSum=0.367;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.03;MQRankSum=1.41;QD=2.14;ReadPosRankSum=0.236;SOR=0.588	GT:AD:DP:GQ:PGT:PID:PL	0/1:66,9:75:99:0|1:10158906_C_T:168,0,4155
+21	10159130	.	G	C	154.96	.	AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=30.99;SOR=3.611	GT:AD:DP:GQ:PL	1/1:0,5:5:15:169,15,0
+21	10159246	.	G	A	245.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.82;ClippingRankSum=-4.190e-01;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.15;MQRankSum=-1.709e+00;QD=3.72;ReadPosRankSum=1.02;SOR=0.065	GT:AD:DP:GQ:PL	0/1:53,13:66:99:253,0,1774
+21	10159282	.	A	G	393.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974e+00;ClippingRankSum=1.44;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=-1.733e+00;QD=7.16;ReadPosRankSum=0.158;SOR=0.166	GT:AD:DP:GQ:PL	0/1:39,16:55:99:401,0,1305
+21	10159336	.	G	A	73.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.34;ClippingRankSum=0.467;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.35;MQRankSum=-1.246e+00;QD=5.26;ReadPosRankSum=1.40;SOR=0.105	GT:AD:DP:GQ:PGT:PID:PL	0/1:11,3:14:81:0|1:10159314_A_G:81,0,704
+21	10159341	.	G	T	94.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;ClippingRankSum=0.296;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.49;MQRankSum=-7.310e-01;QD=9.46;ReadPosRankSum=0.731;SOR=0.223	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,3:10:99:0|1:10159314_A_G:102,0,397
+21	10160074	.	A	G	638.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.096e+00;ClippingRankSum=-6.190e-01;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.85;MQRankSum=-7.840e-01;QD=30.41;ReadPosRankSum=1.69;SOR=2.200	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,16:21:99:0|1:10160056_A_C:646,0,174
+21	10160084	.	G	A	365.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.29;ClippingRankSum=0.578;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.86;MQRankSum=0.578;QD=20.31;ReadPosRankSum=1.38;SOR=0.914	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,10:18:99:0|1:10160056_A_C:373,0,400
+21	10160095	.	T	C	158.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.360e-01;ClippingRankSum=0.071;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.10;MQRankSum=-1.768e+00;QD=11.33;ReadPosRankSum=-1.202e+00;SOR=0.188	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,4:14:99:0|1:10160056_A_C:166,0,481
+21	10160106	.	C	T	262.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.66;ClippingRankSum=-2.780e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.39;MQRankSum=0.597;QD=23.88;ReadPosRankSum=-5.970e-01;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,7:11:99:0|1:10160056_A_C:270,0,207
+21	10160281	.	C	G	58.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.720e-01;ClippingRankSum=0.057;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.85;MQRankSum=1.83;QD=1.63;ReadPosRankSum=-9.160e-01;SOR=0.580	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,3:36:66:0|1:10160281_C_G:66,0,1416
+21	10160292	.	A	T	94.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;ClippingRankSum=1.27;DP=43;ExcessHet=3.0103;FS=2.071;MLEAC=1;MLEAF=0.500;MQ=28.19;MQRankSum=1.44;QD=2.20;ReadPosRankSum=0.732;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,4:43:99:0|1:10160281_C_G:102,0,1620
+21	10160293	.	A	T	95.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.677e+00;ClippingRankSum=-8.160e-01;DP=45;ExcessHet=3.0103;FS=6.287;MLEAC=1;MLEAF=0.500;MQ=28.02;MQRankSum=1.97;QD=2.22;ReadPosRankSum=-1.173e+00;SOR=0.941	GT:AD:DP:GQ:PL	0/1:37,6:45:99:103,0,1553
 21	10160325	.	GT	G	641.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;ClippingRankSum=0.663;DP=83;ExcessHet=3.0103;FS=6.741;MLEAC=1;MLEAF=0.500;MQ=32.86;MQRankSum=2.07;QD=11.26;ReadPosRankSum=-2.050e-01;SOR=0.309	GT:AD:DP:GQ:PL	0/1:24,33:73:99:649,0,858
-21	10160348	.	A	G	389.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.763e+00;ClippingRankSum=1.33;DP=80;ExcessHet=3.0103;FS=6.059;MLEAC=1;MLEAF=0.500;MQ=32.71;MQRankSum=-9.120e-01;QD=4.87;ReadPosRankSum=1.87;SOR=1.662	GT:AD:DP:GQ:PGT:PID:PL	0/1:65,15:80:99:0|1:10160348_A_G:397,0,2633
-21	10160358	.	C	G	1973.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.290e-01;ClippingRankSum=-1.450e-01;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.12;MQRankSum=4.72;QD=27.41;ReadPosRankSum=4.08;SOR=0.815	GT:AD:DP:GQ:PL	0/1:23,49:72:99:1981,0,786
-21	10160367	.	A	G	1658.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.327;ClippingRankSum=2.82;DP=68;ExcessHet=3.0103;FS=2.186;MLEAC=1;MLEAF=0.500;MQ=32.15;MQRankSum=5.15;QD=24.39;ReadPosRankSum=2.42;SOR=1.144	GT:AD:DP:GQ:PL	0/1:24,44:68:99:1666,0,824
-21	10160370	.	G	A	327.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;ClippingRankSum=-8.730e-01;DP=66;ExcessHet=3.0103;FS=9.461;MLEAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=-7.900e-01;QD=4.96;ReadPosRankSum=0.158;SOR=2.147	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,12:66:99:0|1:10160348_A_G:335,0,2315
-21	10160375	.	G	A	208.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.17;ClippingRankSum=0.231;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.21;MQRankSum=2.30;QD=3.26;ReadPosRankSum=-8.960e-01;SOR=0.681	GT:AD:DP:GQ:PL	0/1:53,11:64:99:216,0,1976
-21	10160407	.	C	T	357.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.85;ClippingRankSum=0.947;DP=31;ExcessHet=3.0103;FS=5.747;MLEAC=1;MLEAF=0.500;MQ=29.29;MQRankSum=4.05;QD=11.92;ReadPosRankSum=-2.042e+00;SOR=0.477	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,11:30:99:0|1:10160407_C_T:365,0,672
-21	10160420	.	G	A	40.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.822;ClippingRankSum=-1.187e+00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.20;MQRankSum=2.10;QD=2.90;ReadPosRankSum=-2.282e+00;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,2:14:48:0|1:10160407_C_T:48,0,498
-21	10160562	.	C	A	76.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.517e+00;ClippingRankSum=0.322;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.62;MQRankSum=1.52;QD=9.58;ReadPosRankSum=-9.560e-01;SOR=0.368	GT:AD:DP:GQ:PL	0/1:5,3:8:84:84,0,115
-21	10160578	.	A	G	46.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.268e+00;ClippingRankSum=-4.230e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.20;MQRankSum=-4.230e-01;QD=3.58;ReadPosRankSum=-4.230e-01;SOR=0.124	GT:AD:DP:GQ:PL	0/1:10,3:13:54:54,0,276
-21	10160619	.	T	C	136.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.120e-01;ClippingRankSum=-2.740e-01;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.24;MQRankSum=0.912;QD=4.27;ReadPosRankSum=-6.840e-01;SOR=0.090	GT:AD:DP:GQ:PL	0/1:25,7:32:99:144,0,750
-21	10160642	.	T	C	63.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.721e+00;ClippingRankSum=0.448;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.32;MQRankSum=0.165;QD=1.82;ReadPosRankSum=0.731;SOR=0.037	GT:AD:DP:GQ:PL	0/1:30,5:35:71:71,0,898
-21	10160654	.	T	C	511.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.312e+00;ClippingRankSum=1.35;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.10;MQRankSum=0.855;QD=15.99;ReadPosRankSum=0.019;SOR=0.957	GT:AD:DP:GQ:PL	0/1:14,18:32:99:519,0,428
-21	10160655	.	G	A	32.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.56;ClippingRankSum=0.458;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=0.519;QD=1.09;ReadPosRankSum=0.885;SOR=0.034	GT:AD:DP:GQ:PL	0/1:26,4:30:40:40,0,963
-21	10160659	.	A	T	111.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.04;ClippingRankSum=1.05;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.97;MQRankSum=0.781;QD=3.85;ReadPosRankSum=-1.050e+00;SOR=0.082	GT:AD:DP:GQ:PL	0/1:23,6:29:99:119,0,849
-21	10163127	.	A	C	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.027;ClippingRankSum=-1.584e+00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.75;MQRankSum=1.15;QD=2.99;ReadPosRankSum=0.295;SOR=0.048	GT:AD:DP:GQ:PL	0/1:26,5:31:99:100,0,813
-21	10163218	.	C	A	379.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.18;ClippingRankSum=-6.860e-01;DP=113;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.02;MQRankSum=0.663;QD=3.39;ReadPosRankSum=2.96;SOR=0.056	GT:AD:DP:GQ:PL	0/1:91,21:112:99:387,0,2819
-21	10163303	.	T	C	41.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.422e+00;ClippingRankSum=1.61;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.14;MQRankSum=-1.883e+00;QD=2.60;ReadPosRankSum=-1.345e+00;SOR=0.078	GT:AD:DP:GQ:PL	0/1:13,3:16:49:49,0,426
-21	10163320	.	G	A	123.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=1.38;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.69;MQRankSum=-7.200e-01;QD=20.60;ReadPosRankSum=0.720;SOR=1.329	GT:AD:DP:GQ:PL	0/1:2,4:6:50:131,0,50
-21	10163528	.	A	C	794.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;ClippingRankSum=-2.300e-01;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.94;MQRankSum=0.781;QD=6.11;ReadPosRankSum=-4.530e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:96,34:130:99:802,0,2617
-21	10163675	.	C	G	50.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.17;QD=25.14;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:62,6,0
-21	10163746	.	T	G	182.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.170e-01;ClippingRankSum=0.580;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.12;MQRankSum=-1.467e+00;QD=8.30;ReadPosRankSum=0.990;SOR=0.307	GT:AD:DP:GQ:PL	0/1:14,8:22:99:190,0,448
-21	10163794	.	C	A	136.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.700e-01;ClippingRankSum=-2.340e-01;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.00;MQRankSum=-7.010e-01;QD=3.25;ReadPosRankSum=1.67;SOR=0.035	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,6:42:99:0|1:10163794_C_A:144,0,1394
-21	10163813	.	C	A	142.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.920e-01;ClippingRankSum=0.253;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.68;MQRankSum=0.175;QD=3.66;ReadPosRankSum=1.03;SOR=0.165	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,6:39:99:0|1:10163794_C_A:150,0,1345
-21	10163887	.	C	G	61.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.39;ClippingRankSum=-7.610e-01;DP=21;ExcessHet=3.0103;FS=5.935;MLEAC=1;MLEAF=0.500;MQ=24.89;MQRankSum=2.64;QD=2.93;ReadPosRankSum=1.48;SOR=2.655	GT:AD:DP:GQ:PL	0/1:17,4:21:69:69,0,362
-21	10166996	.	T	A	141.71	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;ClippingRankSum=0.747;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.69;MQRankSum=-7.470e-01;QD=17.71;ReadPosRankSum=-7.470e-01;SOR=0.595	GT:AD:DP:GQ:PL	0/1:1,7:8:6:149,0,6
-21	10177875	.	G	A	449.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.63;ClippingRankSum=-8.790e-01;DP=48;ExcessHet=3.0103;FS=2.419;MLEAC=1;MLEAF=0.500;MQ=22.71;MQRankSum=-8.170e-01;QD=9.37;ReadPosRankSum=1.25;SOR=1.085	GT:AD:DP:GQ:PL	0/1:26,22:48:99:457,0,569
-21	10181184	.	T	C	289.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.691e+00;ClippingRankSum=-1.749e+00;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.09;MQRankSum=0.538;QD=18.10;ReadPosRankSum=-4.040e-01;SOR=2.584	GT:AD:DP:GQ:PL	0/1:3,13:16:31:297,0,31
-21	10181499	.	C	A	437.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;ClippingRankSum=-1.292e+00;DP=86;ExcessHet=3.0103;FS=23.447;MLEAC=1;MLEAF=0.500;MQ=22.96;MQRankSum=-8.390e-01;QD=5.15;ReadPosRankSum=0.617;SOR=3.692	GT:AD:DP:GQ:PL	0/1:66,19:85:99:445,0,1552
-21	10181512	.	G	A	44.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.20;ClippingRankSum=-4.200e-01;DP=101;ExcessHet=3.0103;FS=15.212;MLEAC=1;MLEAF=0.500;MQ=22.60;MQRankSum=0.799;QD=0.45;ReadPosRankSum=-2.460e-01;SOR=2.931	GT:AD:DP:GQ:PL	0/1:87,13:100:52:52,0,3369
-21	10181557	.	A	G	248.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.726e+00;ClippingRankSum=0.359;DP=90;ExcessHet=3.0103;FS=23.998;MLEAC=1;MLEAF=0.500;MQ=22.77;MQRankSum=0.310;QD=2.79;ReadPosRankSum=-8.600e-01;SOR=3.332	GT:AD:DP:GQ:PL	0/1:69,20:89:99:256,0,1622
-21	10181781	.	A	G	36.61	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=0.736;QD=12.20;ReadPosRankSum=-7.360e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:1,2:3:18:44,0,18
-21	10181956	.	T	C	32.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=1.03;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.29;MQRankSum=0.00;QD=8.15;ReadPosRankSum=-1.026e+00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:39:40,0,39
-21	10183557	.	T	C	376.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.728e+00;ClippingRankSum=-1.680e-01;DP=37;ExcessHet=3.0103;FS=4.167;MLEAC=1;MLEAF=0.500;MQ=21.44;MQRankSum=-4.130e+00;QD=10.18;ReadPosRankSum=1.26;SOR=1.811	GT:AD:DP:GQ:PL	0/1:17,20:37:99:384,0,322
-21	10184113	.	G	C	56.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384e+00;ClippingRankSum=0.789;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.61;MQRankSum=1.52;QD=1.32;ReadPosRankSum=-7.890e-01;SOR=0.963	GT:AD:DP:GQ:PL	0/1:37,6:43:64:64,0,1530
-21	10184126	.	T	C	1422.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.350e-01;ClippingRankSum=1.56;DP=58;ExcessHet=3.0103;FS=33.567;MLEAC=1;MLEAF=0.500;MQ=31.55;MQRankSum=2.08;QD=24.96;ReadPosRankSum=1.70;SOR=5.967	GT:AD:DP:GQ:PL	0/1:21,36:57:99:1430,0,449
-21	10184131	.	G	A	242.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.94;ClippingRankSum=1.40;DP=60;ExcessHet=3.0103;FS=4.819;MLEAC=1;MLEAF=0.500;MQ=32.06;MQRankSum=1.05;QD=4.11;ReadPosRankSum=1.62;SOR=2.179	GT:AD:DP:GQ:PL	0/1:46,13:59:99:250,0,1887
-21	10184135	.	T	A	777.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.59;ClippingRankSum=-1.445e+00;DP=64;ExcessHet=3.0103;FS=14.535;MLEAC=1;MLEAF=0.500;MQ=32.10;MQRankSum=1.68;QD=12.34;ReadPosRankSum=-1.110e+00;SOR=3.903	GT:AD:DP:GQ:PL	0/1:37,26:63:99:785,0,1407
-21	10184191	.	C	G	678.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.959e+00;ClippingRankSum=-1.375e+00;DP=62;ExcessHet=3.0103;FS=5.333;MLEAC=1;MLEAF=0.500;MQ=34.12;MQRankSum=-1.000e-01;QD=11.12;ReadPosRankSum=1.88;SOR=2.156	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,20:61:99:0|1:10184191_C_G:686,0,1574
-21	10184208	.	C	T	713.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.11;ClippingRankSum=1.90;DP=54;ExcessHet=3.0103;FS=2.831;MLEAC=1;MLEAF=0.500;MQ=33.12;MQRankSum=0.248;QD=13.46;ReadPosRankSum=1.31;SOR=1.584	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,20:53:99:0|1:10184191_C_G:721,0,1402
-21	10184233	.	T	C	1073.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.144;ClippingRankSum=0.722;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.11;MQRankSum=1.63;QD=30.67;ReadPosRankSum=-9.280e-01;SOR=2.649	GT:AD:DP:GQ:PL	0/1:7,28:35:99:1081,0,119
-21	10184407	.	G	A	165.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.80;ClippingRankSum=0.540;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.86;MQRankSum=-4.200e-01;QD=5.91;ReadPosRankSum=0.540;SOR=0.922	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,5:28:99:0|1:10184407_G_A:173,0,1017
-21	10184428	.	T	G	284.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.039e+00;ClippingRankSum=0.246;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.10;MQRankSum=-1.660e-01;QD=4.25;ReadPosRankSum=-4.040e-01;SOR=0.593	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,13:67:99:0|1:10184407_G_A:292,0,2046
-21	10184512	.	C	T	542.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.847;ClippingRankSum=-1.490e-01;DP=120;ExcessHet=3.0103;FS=9.178;MLEAC=1;MLEAF=0.500;MQ=36.56;MQRankSum=-8.340e-01;QD=4.52;ReadPosRankSum=-1.796e+00;SOR=0.975	GT:AD:DP:GQ:PL	0/1:95,25:120:99:550,0,3224
-21	10184685	.	C	T	142.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.45;ClippingRankSum=-6.330e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.05;MQRankSum=-2.383e+00;QD=14.26;ReadPosRankSum=0.00;SOR=0.412	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,4:10:99:0|1:10184685_C_T:150,0,736
-21	10184710	.	A	G	313.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083e+00;ClippingRankSum=0.077;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.16;MQRankSum=-2.289e+00;QD=11.61;ReadPosRankSum=0.129;SOR=0.245	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,9:27:99:0|1:10184685_C_T:321,0,2030
-21	10184735	.	A	C	328.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.359e+00;ClippingRankSum=-1.160e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.62;MQRankSum=-1.939e+00;QD=8.65;ReadPosRankSum=1.38;SOR=0.134	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,10:38:99:0|1:10184685_C_T:336,0,2629
-21	10184747	.	A	G	345.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.80;ClippingRankSum=0.343;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.82;MQRankSum=-2.146e+00;QD=8.23;ReadPosRankSum=0.572;SOR=0.132	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,11:42:99:0|1:10184685_C_T:353,0,2657
-21	10184809	.	G	A	37.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.810e-01;ClippingRankSum=0.732;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.34;MQRankSum=-8.990e-01;QD=0.87;ReadPosRankSum=-1.735e+00;SOR=0.016	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,4:43:45:0|1:10184685_C_T:45,0,2769
-21	10185234	.	A	C	41.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.583;ClippingRankSum=0.397;DP=33;ExcessHet=3.0103;FS=1.830;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-1.170e-01;QD=1.26;ReadPosRankSum=-1.237e+00;SOR=1.294	GT:AD:DP:GQ:PL	0/1:27,6:33:49:49,0,569
-21	10186902	.	T	G	286.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.730;ClippingRankSum=-1.477e+00;DP=333;ExcessHet=3.0103;FS=5.135;MLEAC=1;MLEAF=0.500;MQ=21.53;MQRankSum=2.06;QD=0.86;ReadPosRankSum=-8.230e-01;SOR=1.261	GT:AD:DP:GQ:PL	0/1:304,29:333:99:294,0,12721
-21	10186905	.	G	A	277.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.57;ClippingRankSum=-1.706e+00;DP=339;ExcessHet=3.0103;FS=4.883;MLEAC=1;MLEAF=0.500;MQ=21.73;MQRankSum=1.99;QD=0.82;ReadPosRankSum=-6.100e-02;SOR=1.186	GT:AD:DP:GQ:PL	0/1:308,29:339:99:285,0,12784
-21	10186932	.	T	C	184.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.600e-01;ClippingRankSum=-3.180e-01;DP=252;ExcessHet=3.0103;FS=14.092;MLEAC=1;MLEAF=0.500;MQ=23.85;MQRankSum=-9.680e-01;QD=0.76;ReadPosRankSum=0.424;SOR=1.488	GT:AD:DP:GQ:PL	0/1:211,33:244:99:192,0,5140
+21	10160348	.	A	G	389.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.763e+00;ClippingRankSum=1.33;DP=80;ExcessHet=3.0103;FS=6.059;MLEAC=1;MLEAF=0.500;MQ=32.71;MQRankSum=-9.120e-01;QD=4.87;ReadPosRankSum=1.87;SOR=1.662	GT:AD:DP:GQ:PGT:PID:PL	0/1:65,15:80:99:0|1:10160348_A_G:397,0,2633
+21	10160358	.	C	G	1973.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.290e-01;ClippingRankSum=-1.450e-01;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.12;MQRankSum=4.72;QD=27.41;ReadPosRankSum=4.08;SOR=0.815	GT:AD:DP:GQ:PL	0/1:23,49:72:99:1981,0,786
+21	10160367	.	A	G	1658.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.327;ClippingRankSum=2.82;DP=68;ExcessHet=3.0103;FS=2.186;MLEAC=1;MLEAF=0.500;MQ=32.15;MQRankSum=5.15;QD=24.39;ReadPosRankSum=2.42;SOR=1.144	GT:AD:DP:GQ:PL	0/1:24,44:68:99:1666,0,824
+21	10160370	.	G	A	327.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;ClippingRankSum=-8.730e-01;DP=66;ExcessHet=3.0103;FS=9.461;MLEAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=-7.900e-01;QD=4.96;ReadPosRankSum=0.158;SOR=2.147	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,12:66:99:0|1:10160348_A_G:335,0,2315
+21	10160375	.	G	A	208.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.17;ClippingRankSum=0.231;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.21;MQRankSum=2.30;QD=3.26;ReadPosRankSum=-8.960e-01;SOR=0.681	GT:AD:DP:GQ:PL	0/1:53,11:64:99:216,0,1976
+21	10160407	.	C	T	357.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.85;ClippingRankSum=0.947;DP=31;ExcessHet=3.0103;FS=5.747;MLEAC=1;MLEAF=0.500;MQ=29.29;MQRankSum=4.05;QD=11.92;ReadPosRankSum=-2.042e+00;SOR=0.477	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,11:30:99:0|1:10160407_C_T:365,0,672
+21	10160420	.	G	A	40.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.822;ClippingRankSum=-1.187e+00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.20;MQRankSum=2.10;QD=2.90;ReadPosRankSum=-2.282e+00;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,2:14:48:0|1:10160407_C_T:48,0,498
+21	10160562	.	C	A	76.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.517e+00;ClippingRankSum=0.322;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.62;MQRankSum=1.52;QD=9.58;ReadPosRankSum=-9.560e-01;SOR=0.368	GT:AD:DP:GQ:PL	0/1:5,3:8:84:84,0,115
+21	10160578	.	A	G	46.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.268e+00;ClippingRankSum=-4.230e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.20;MQRankSum=-4.230e-01;QD=3.59;ReadPosRankSum=-4.230e-01;SOR=0.124	GT:AD:DP:GQ:PL	0/1:10,3:13:54:54,0,276
+21	10160619	.	T	C	136.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.120e-01;ClippingRankSum=-2.740e-01;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.24;MQRankSum=0.912;QD=4.27;ReadPosRankSum=-6.840e-01;SOR=0.090	GT:AD:DP:GQ:PL	0/1:25,7:32:99:144,0,750
+21	10160642	.	T	C	63.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.721e+00;ClippingRankSum=0.448;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.32;MQRankSum=0.165;QD=1.82;ReadPosRankSum=0.731;SOR=0.037	GT:AD:DP:GQ:PL	0/1:30,5:35:71:71,0,898
+21	10160654	.	T	C	511.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.312e+00;ClippingRankSum=1.35;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.10;MQRankSum=0.855;QD=15.99;ReadPosRankSum=0.019;SOR=0.957	GT:AD:DP:GQ:PL	0/1:14,18:32:99:519,0,428
+21	10160655	.	G	A	32.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.56;ClippingRankSum=0.458;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=0.519;QD=1.09;ReadPosRankSum=0.885;SOR=0.034	GT:AD:DP:GQ:PL	0/1:26,4:30:40:40,0,963
+21	10160659	.	A	T	111.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.04;ClippingRankSum=1.05;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.97;MQRankSum=0.781;QD=3.85;ReadPosRankSum=-1.050e+00;SOR=0.082	GT:AD:DP:GQ:PL	0/1:23,6:29:99:119,0,849
+21	10163127	.	A	C	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.027;ClippingRankSum=-1.584e+00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.75;MQRankSum=1.15;QD=2.99;ReadPosRankSum=0.295;SOR=0.048	GT:AD:DP:GQ:PL	0/1:26,5:31:99:100,0,813
+21	10163218	.	C	A	379.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.18;ClippingRankSum=-6.860e-01;DP=113;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.02;MQRankSum=0.663;QD=3.39;ReadPosRankSum=2.96;SOR=0.056	GT:AD:DP:GQ:PL	0/1:91,21:112:99:387,0,2819
+21	10163303	.	T	C	41.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.422e+00;ClippingRankSum=1.61;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.14;MQRankSum=-1.883e+00;QD=2.60;ReadPosRankSum=-1.345e+00;SOR=0.078	GT:AD:DP:GQ:PL	0/1:13,3:16:49:49,0,426
+21	10163320	.	G	A	123.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=1.38;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.69;MQRankSum=-7.200e-01;QD=20.61;ReadPosRankSum=0.720;SOR=1.329	GT:AD:DP:GQ:PL	0/1:2,4:6:50:131,0,50
+21	10163528	.	A	C	794.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;ClippingRankSum=-2.300e-01;DP=130;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.94;MQRankSum=0.781;QD=6.11;ReadPosRankSum=-4.530e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:96,34:130:99:802,0,2617
+21	10163675	.	C	G	50.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.17;QD=25.16;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:62,6,0
+21	10163746	.	T	G	182.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.170e-01;ClippingRankSum=0.580;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.12;MQRankSum=-1.467e+00;QD=8.30;ReadPosRankSum=0.990;SOR=0.307	GT:AD:DP:GQ:PL	0/1:14,8:22:99:190,0,448
+21	10163794	.	C	A	136.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.700e-01;ClippingRankSum=-2.340e-01;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.00;MQRankSum=-7.010e-01;QD=3.25;ReadPosRankSum=1.67;SOR=0.035	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,6:42:99:0|1:10163794_C_A:144,0,1394
+21	10163813	.	C	A	142.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.920e-01;ClippingRankSum=0.253;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.68;MQRankSum=0.175;QD=3.66;ReadPosRankSum=1.03;SOR=0.165	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,6:39:99:0|1:10163794_C_A:150,0,1345
+21	10163887	.	C	G	61.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.39;ClippingRankSum=-7.610e-01;DP=21;ExcessHet=3.0103;FS=5.935;MLEAC=1;MLEAF=0.500;MQ=24.89;MQRankSum=2.64;QD=2.94;ReadPosRankSum=1.48;SOR=2.655	GT:AD:DP:GQ:PL	0/1:17,4:21:69:69,0,362
+21	10166996	.	T	A	141.75	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;ClippingRankSum=0.747;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.69;MQRankSum=-7.470e-01;QD=17.72;ReadPosRankSum=-7.470e-01;SOR=0.595	GT:AD:DP:GQ:PL	0/1:1,7:8:6:149,0,6
+21	10177875	.	G	A	449.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.63;ClippingRankSum=-8.790e-01;DP=48;ExcessHet=3.0103;FS=2.419;MLEAC=1;MLEAF=0.500;MQ=22.71;MQRankSum=-8.170e-01;QD=9.37;ReadPosRankSum=1.25;SOR=1.085	GT:AD:DP:GQ:PL	0/1:26,22:48:99:457,0,569
+21	10181184	.	T	C	289.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.691e+00;ClippingRankSum=-1.749e+00;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.09;MQRankSum=0.538;QD=18.10;ReadPosRankSum=-4.040e-01;SOR=2.584	GT:AD:DP:GQ:PL	0/1:3,13:16:31:297,0,31
+21	10181499	.	C	A	437.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;ClippingRankSum=-1.292e+00;DP=86;ExcessHet=3.0103;FS=23.447;MLEAC=1;MLEAF=0.500;MQ=22.96;MQRankSum=-8.390e-01;QD=5.15;ReadPosRankSum=0.617;SOR=3.692	GT:AD:DP:GQ:PL	0/1:66,19:85:99:445,0,1552
+21	10181512	.	G	A	44.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.20;ClippingRankSum=-4.200e-01;DP=101;ExcessHet=3.0103;FS=15.212;MLEAC=1;MLEAF=0.500;MQ=22.60;MQRankSum=0.799;QD=0.45;ReadPosRankSum=-2.460e-01;SOR=2.931	GT:AD:DP:GQ:PL	0/1:87,13:100:52:52,0,3369
+21	10181557	.	A	G	248.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.726e+00;ClippingRankSum=0.359;DP=90;ExcessHet=3.0103;FS=23.998;MLEAC=1;MLEAF=0.500;MQ=22.77;MQRankSum=0.310;QD=2.79;ReadPosRankSum=-8.600e-01;SOR=3.332	GT:AD:DP:GQ:PL	0/1:69,20:89:99:256,0,1622
+21	10181781	.	A	G	36.65	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.00;MQRankSum=0.736;QD=12.22;ReadPosRankSum=-7.360e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:1,2:3:18:44,0,18
+21	10181956	.	T	C	32.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=1.03;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.29;MQRankSum=0.00;QD=8.16;ReadPosRankSum=-1.026e+00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:39:40,0,39
+21	10183557	.	T	C	376.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.728e+00;ClippingRankSum=-1.680e-01;DP=37;ExcessHet=3.0103;FS=4.167;MLEAC=1;MLEAF=0.500;MQ=21.44;MQRankSum=-4.130e+00;QD=10.18;ReadPosRankSum=1.26;SOR=1.811	GT:AD:DP:GQ:PL	0/1:17,20:37:99:384,0,322
+21	10184113	.	G	C	56.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384e+00;ClippingRankSum=0.789;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.61;MQRankSum=1.52;QD=1.32;ReadPosRankSum=-7.890e-01;SOR=0.963	GT:AD:DP:GQ:PL	0/1:37,6:43:64:64,0,1530
+21	10184126	.	T	C	1422.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.350e-01;ClippingRankSum=1.56;DP=58;ExcessHet=3.0103;FS=33.567;MLEAC=1;MLEAF=0.500;MQ=31.55;MQRankSum=2.08;QD=24.96;ReadPosRankSum=1.70;SOR=5.967	GT:AD:DP:GQ:PL	0/1:21,36:57:99:1430,0,449
+21	10184131	.	G	A	242.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.94;ClippingRankSum=1.40;DP=60;ExcessHet=3.0103;FS=4.819;MLEAC=1;MLEAF=0.500;MQ=32.06;MQRankSum=1.05;QD=4.11;ReadPosRankSum=1.62;SOR=2.179	GT:AD:DP:GQ:PL	0/1:46,13:59:99:250,0,1887
+21	10184135	.	T	A	777.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.59;ClippingRankSum=-1.445e+00;DP=64;ExcessHet=3.0103;FS=14.535;MLEAC=1;MLEAF=0.500;MQ=32.10;MQRankSum=1.68;QD=12.34;ReadPosRankSum=-1.110e+00;SOR=3.903	GT:AD:DP:GQ:PL	0/1:37,26:63:99:785,0,1407
+21	10184191	.	C	G	678.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.959e+00;ClippingRankSum=-1.375e+00;DP=62;ExcessHet=3.0103;FS=5.333;MLEAC=1;MLEAF=0.500;MQ=34.12;MQRankSum=-1.000e-01;QD=11.13;ReadPosRankSum=1.88;SOR=2.156	GT:AD:DP:GQ:PGT:PID:PL	0/1:41,20:61:99:0|1:10184191_C_G:686,0,1574
+21	10184208	.	C	T	713.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.11;ClippingRankSum=1.90;DP=54;ExcessHet=3.0103;FS=2.831;MLEAC=1;MLEAF=0.500;MQ=33.12;MQRankSum=0.248;QD=13.46;ReadPosRankSum=1.31;SOR=1.584	GT:AD:DP:GQ:PGT:PID:PL	0/1:33,20:53:99:0|1:10184191_C_G:721,0,1402
+21	10184233	.	T	C	1073.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.144;ClippingRankSum=0.722;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.11;MQRankSum=1.63;QD=30.68;ReadPosRankSum=-9.280e-01;SOR=2.649	GT:AD:DP:GQ:PL	0/1:7,28:35:99:1081,0,119
+21	10184407	.	G	A	165.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.80;ClippingRankSum=0.540;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.86;MQRankSum=-4.200e-01;QD=5.92;ReadPosRankSum=0.540;SOR=0.922	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,5:28:99:0|1:10184407_G_A:173,0,1017
+21	10184428	.	T	G	284.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.039e+00;ClippingRankSum=0.246;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.10;MQRankSum=-1.660e-01;QD=4.25;ReadPosRankSum=-4.040e-01;SOR=0.593	GT:AD:DP:GQ:PGT:PID:PL	0/1:54,13:67:99:0|1:10184407_G_A:292,0,2046
+21	10184512	.	C	T	542.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.847;ClippingRankSum=-1.490e-01;DP=120;ExcessHet=3.0103;FS=9.178;MLEAC=1;MLEAF=0.500;MQ=36.56;MQRankSum=-8.340e-01;QD=4.52;ReadPosRankSum=-1.796e+00;SOR=0.975	GT:AD:DP:GQ:PL	0/1:95,25:120:99:550,0,3224
+21	10184685	.	C	T	142.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.45;ClippingRankSum=-6.330e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.05;MQRankSum=-2.383e+00;QD=14.26;ReadPosRankSum=0.00;SOR=0.412	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,4:10:99:0|1:10184685_C_T:150,0,736
+21	10184710	.	A	G	313.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083e+00;ClippingRankSum=0.077;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.16;MQRankSum=-2.289e+00;QD=11.62;ReadPosRankSum=0.129;SOR=0.245	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,9:27:99:0|1:10184685_C_T:321,0,2030
+21	10184735	.	A	C	328.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.359e+00;ClippingRankSum=-1.160e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.62;MQRankSum=-1.939e+00;QD=8.65;ReadPosRankSum=1.38;SOR=0.134	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,10:38:99:0|1:10184685_C_T:336,0,2629
+21	10184747	.	A	G	345.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.80;ClippingRankSum=0.343;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.82;MQRankSum=-2.146e+00;QD=8.23;ReadPosRankSum=0.572;SOR=0.132	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,11:42:99:0|1:10184685_C_T:353,0,2657
+21	10184809	.	G	A	37.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.810e-01;ClippingRankSum=0.732;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.34;MQRankSum=-8.990e-01;QD=0.88;ReadPosRankSum=-1.735e+00;SOR=0.016	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,4:43:45:0|1:10184685_C_T:45,0,2769
+21	10185234	.	A	C	41.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.583;ClippingRankSum=0.397;DP=33;ExcessHet=3.0103;FS=1.830;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-1.170e-01;QD=1.26;ReadPosRankSum=-1.237e+00;SOR=1.294	GT:AD:DP:GQ:PL	0/1:27,6:33:49:49,0,569
+21	10186902	.	T	G	286.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.730;ClippingRankSum=-1.477e+00;DP=333;ExcessHet=3.0103;FS=5.135;MLEAC=1;MLEAF=0.500;MQ=21.53;MQRankSum=2.06;QD=0.86;ReadPosRankSum=-8.230e-01;SOR=1.261	GT:AD:DP:GQ:PL	0/1:304,29:333:99:294,0,12721
+21	10186905	.	G	A	277.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.57;ClippingRankSum=-1.706e+00;DP=339;ExcessHet=3.0103;FS=4.883;MLEAC=1;MLEAF=0.500;MQ=21.73;MQRankSum=1.99;QD=0.82;ReadPosRankSum=-6.100e-02;SOR=1.186	GT:AD:DP:GQ:PL	0/1:308,29:339:99:285,0,12784
+21	10186932	.	T	C	184.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.600e-01;ClippingRankSum=-3.180e-01;DP=252;ExcessHet=3.0103;FS=14.092;MLEAC=1;MLEAF=0.500;MQ=23.85;MQRankSum=-9.680e-01;QD=0.76;ReadPosRankSum=0.424;SOR=1.488	GT:AD:DP:GQ:PL	0/1:211,33:244:99:192,0,5140
 21	10187060	.	AT	A	121.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.040e-01;ClippingRankSum=-5.260e-01;DP=37;ExcessHet=3.0103;FS=2.634;MLEAC=1;MLEAF=0.500;MQ=28.52;MQRankSum=0.968;QD=4.50;ReadPosRankSum=-2.800e-02;SOR=1.426	GT:AD:DP:GQ:PL	0/1:20,7:27:99:129,0,500
-21	10187227	.	T	A	35.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.797;ClippingRankSum=0.614;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.11;MQRankSum=-9.460e-01;QD=0.43;ReadPosRankSum=1.66;SOR=0.713	GT:AD:DP:GQ:PL	0/1:75,7:82:43:43,0,2649
+21	10187227	.	T	A	35.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.797;ClippingRankSum=0.614;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.11;MQRankSum=-9.460e-01;QD=0.43;ReadPosRankSum=1.66;SOR=0.713	GT:AD:DP:GQ:PL	0/1:75,7:82:43:43,0,2649
 21	10187289	.	CTA	C	754.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.789e+00;ClippingRankSum=0.886;DP=237;ExcessHet=3.0103;FS=20.102;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=-9.186e+00;QD=3.24;ReadPosRankSum=-8.910e-01;SOR=0.962	GT:AD:DP:GQ:PL	0/1:194,39:237:99:762,0,7179
-21	10187291	.	A	C	7026.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.672e+00;ClippingRankSum=0.134;DP=237;ExcessHet=3.0103;FS=20.102;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=8.83;QD=29.65;ReadPosRankSum=0.345;SOR=1.151	GT:AD:DP:GQ:PL	0/1:43,194:237:99:7034,0,991
-21	10187293	.	A	C	7823.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.030e-01;ClippingRankSum=-1.000e-03;DP=237;ExcessHet=3.0103;FS=1.595;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=-1.925e+00;QD=33.01;ReadPosRankSum=2.95;SOR=0.503	GT:AD:DP:GQ:PL	0/1:30,207:237:99:7831,0,476
-21	10187295	.	A	C	833.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.307e+00;ClippingRankSum=-8.290e-01;DP=237;ExcessHet=3.0103;FS=26.080;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=-9.806e+00;QD=3.52;ReadPosRankSum=1.59;SOR=1.213	GT:AD:DP:GQ:PL	0/1:198,39:237:99:841,0,7347
-21	10187342	.	C	A	226.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.45;ClippingRankSum=-8.170e-01;DP=135;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=31.37;MQRankSum=-6.604e+00;QD=1.68;ReadPosRankSum=-5.160e-01;SOR=0.868	GT:AD:DP:GQ:PL	0/1:109,26:135:99:234,0,3404
-21	10187676	.	T	C	36.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.572;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.90;MQRankSum=-5.720e-01;QD=4.58;ReadPosRankSum=0.572;SOR=0.169	GT:AD:DP:GQ:PL	0/1:6,2:8:44:44,0,162
-21	10189527	.	G	C	530.03	.	AC=2;AF=1.00;AN=2;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.96;QD=33.13;SOR=5.670	GT:AD:DP:GQ:PL	1/1:0,16:16:48:544,48,0
+21	10187291	.	A	C	7026.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.672e+00;ClippingRankSum=0.134;DP=237;ExcessHet=3.0103;FS=20.102;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=8.83;QD=29.65;ReadPosRankSum=0.345;SOR=1.151	GT:AD:DP:GQ:PL	0/1:43,194:237:99:7034,0,991
+21	10187293	.	A	C	7823.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.030e-01;ClippingRankSum=-1.000e-03;DP=237;ExcessHet=3.0103;FS=1.595;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=-1.925e+00;QD=33.01;ReadPosRankSum=2.95;SOR=0.503	GT:AD:DP:GQ:PL	0/1:30,207:237:99:7831,0,476
+21	10187295	.	A	C	833.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.307e+00;ClippingRankSum=-8.290e-01;DP=237;ExcessHet=3.0103;FS=26.080;MLEAC=1;MLEAF=0.500;MQ=34.48;MQRankSum=-9.806e+00;QD=3.52;ReadPosRankSum=1.59;SOR=1.213	GT:AD:DP:GQ:PL	0/1:198,39:237:99:841,0,7347
+21	10187342	.	C	A	226.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.45;ClippingRankSum=-8.170e-01;DP=135;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=31.37;MQRankSum=-6.604e+00;QD=1.68;ReadPosRankSum=-5.160e-01;SOR=0.868	GT:AD:DP:GQ:PL	0/1:109,26:135:99:234,0,3404
+21	10187676	.	T	C	36.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.572;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.90;MQRankSum=-5.720e-01;QD=4.58;ReadPosRankSum=0.572;SOR=0.169	GT:AD:DP:GQ:PL	0/1:6,2:8:44:44,0,162
+21	10189527	.	G	C	530.06	.	AC=2;AF=1.00;AN=2;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.96;QD=33.13;SOR=5.670	GT:AD:DP:GQ:PL	1/1:0,16:16:48:544,48,0
 21	10189841	.	AT	A	95.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.45;ClippingRankSum=0.288;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.75;MQRankSum=-6.390e-01;QD=1.24;ReadPosRankSum=0.625;SOR=0.593	GT:AD:DP:GQ:PL	0/1:65,12:77:99:103,0,1495
-21	10190053	.	T	G	115.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380e+00;ClippingRankSum=-7.200e-01;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.51;MQRankSum=-7.200e-01;QD=19.27;ReadPosRankSum=1.38;SOR=1.329	GT:AD:DP:GQ:PL	0/1:2,4:6:56:123,0,56
+21	10190053	.	T	G	115.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380e+00;ClippingRankSum=-7.200e-01;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.51;MQRankSum=-7.200e-01;QD=19.27;ReadPosRankSum=1.38;SOR=1.329	GT:AD:DP:GQ:PL	0/1:2,4:6:56:123,0,56
 21	10191515	.	GT	G	68.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;ClippingRankSum=0.602;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.50;MQRankSum=0.231;QD=3.61;ReadPosRankSum=0.602;SOR=1.179	GT:AD:DP:GQ:PL	0/1:14,5:19:76:76,0,311
-21	10191583	.	G	A	100.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.190e-01;ClippingRankSum=-2.120e-01;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.26;MQRankSum=1.63;QD=7.19;ReadPosRankSum=0.495;SOR=0.412	GT:AD:DP:GQ:PL	0/1:10,4:14:99:108,0,264
-21	10192215	.	G	C	271.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.76;ClippingRankSum=1.05;DP=61;ExcessHet=3.0103;FS=4.151;MLEAC=1;MLEAF=0.500;MQ=26.83;MQRankSum=-2.490e-01;QD=4.45;ReadPosRankSum=-9.570e-01;SOR=1.461	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,17:61:99:0|1:10192215_G_C:279,0,1223
-21	10192716	.	T	C	117.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.525e+00;ClippingRankSum=-1.250e-01;DP=32;ExcessHet=3.0103;FS=39.428;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=1.58;QD=3.79;ReadPosRankSum=0.575;SOR=3.892	GT:AD:DP:GQ:PL	0/1:25,6:31:99:125,0,574
-21	10192752	.	T	C	92.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.119e+00;ClippingRankSum=-4.800e-01;DP=28;ExcessHet=3.0103;FS=23.278;MLEAC=1;MLEAF=0.500;MQ=23.24;MQRankSum=0.900;QD=3.31;ReadPosRankSum=2.22;SOR=3.588	GT:AD:DP:GQ:PL	0/1:23,5:28:99:100,0,532
-21	10193671	.	C	T	186.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.61;ClippingRankSum=0.606;DP=26;ExcessHet=3.0103;FS=7.204;MLEAC=1;MLEAF=0.500;MQ=24.20;MQRankSum=-8.700e-01;QD=7.18;ReadPosRankSum=0.501;SOR=2.409	GT:AD:DP:GQ:PL	0/1:16,10:26:99:194,0,467
-21	10193672	.	G	C	108.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=-2.890e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.12;MQRankSum=0.636;QD=4.18;ReadPosRankSum=-9.830e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:19,7:26:99:116,0,601
-21	10194878	.	C	T	97.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.396;ClippingRankSum=-5.780e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.62;MQRankSum=0.335;QD=4.07;ReadPosRankSum=1.73;SOR=0.646	GT:AD:DP:GQ:PL	0/1:20,4:26:99:105,0,983
-21	10194880	.	C	T	140.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.07;ClippingRankSum=-5.450e-01;DP=28;ExcessHet=3.0103;FS=2.276;MLEAC=1;MLEAF=0.500;MQ=31.62;MQRankSum=-1.524e+00;QD=10.82;ReadPosRankSum=-5.450e-01;SOR=1.535	GT:AD:DP:GQ:PL	0/1:7,6:14:99:148,0,706
-21	10196002	.	G	C	164.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.513e+00;ClippingRankSum=0.804;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.33;MQRankSum=0.910;QD=1.51;ReadPosRankSum=0.567;SOR=0.042	GT:AD:DP:GQ:PL	0/1:91,18:109:99:172,0,2263
-21	10196308	.	C	CA	1064.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.600e-01;ClippingRankSum=2.37;DP=328;ExcessHet=3.0103;FS=7.872;MLEAC=1;MLEAF=0.500;MQ=23.74;MQRankSum=1.59;QD=3.55;ReadPosRankSum=2.23;SOR=0.491	GT:AD:DP:GQ:PL	0/1:244,56:328:99:1072,0,6831
-21	10196317	.	A	G	173.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.982e+00;ClippingRankSum=0.314;DP=352;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.73;MQRankSum=0.737;QD=0.49;ReadPosRankSum=1.23;SOR=0.705	GT:AD:DP:GQ:PL	0/1:320,32:352:99:181,0,13193
-21	10196318	.	G	A	343.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.68;ClippingRankSum=0.197;DP=352;ExcessHet=3.0103;FS=0.630;MLEAC=1;MLEAF=0.500;MQ=23.73;MQRankSum=0.674;QD=1.00;ReadPosRankSum=1.66;SOR=0.608	GT:AD:DP:GQ:PL	0/1:313,32:352:99:351,0,12992
-21	10196368	.	G	GT	1337.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.830e-01;ClippingRankSum=1.58;DP=206;ExcessHet=3.0103;FS=4.452;MLEAC=1;MLEAF=0.500;MQ=23.66;MQRankSum=-2.712e+00;QD=10.53;ReadPosRankSum=-4.740e-01;SOR=0.399	GT:AD:DP:GQ:PL	0/1:76,51:138:99:1345,0,1733
-21	10196397	.	T	C	73.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.487e+00;ClippingRankSum=0.934;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.60;MQRankSum=0.102;QD=1.15;ReadPosRankSum=0.453;SOR=0.791	GT:AD:DP:GQ:PL	0/1:54,10:64:81:81,0,1360
-21	10196559	.	G	A	95.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.472;ClippingRankSum=0.766;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.09;MQRankSum=-1.150e-01;QD=1.68;ReadPosRankSum=2.63;SOR=0.051	GT:AD:DP:GQ:PL	0/1:47,10:57:99:103,0,1138
-21	10199880	.	A	AACAAACATTCAGACCACAGCAGGAGTGTTCTGGAATCCTATGTGAGG	160.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.960e-01;ClippingRankSum=0.087;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.10;MQRankSum=-5.630e-01;QD=2.01;ReadPosRankSum=-1.689e+00;SOR=1.270	GT:AD:DP:GQ:PL	0/1:79,1:80:99:168,0,3693
-21	10200470	.	G	T	73.10	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.79;QD=18.27;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:87,12,0
-21	10200543	.	C	A	98.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;ClippingRankSum=-1.113e+00;DP=22;ExcessHet=3.0103;FS=7.929;MLEAC=1;MLEAF=0.500;MQ=23.00;MQRankSum=-1.361e+00;QD=4.93;ReadPosRankSum=-1.938e+00;SOR=1.093	GT:AD:DP:GQ:PL	0/1:14,6:20:99:106,0,328
-21	10200735	.	T	A	513.61	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.59;ClippingRankSum=1.16;DP=21;ExcessHet=3.0103;FS=18.016;MLEAC=1;MLEAF=0.500;MQ=28.99;MQRankSum=0.953;QD=25.68;ReadPosRankSum=0.423;SOR=5.782	GT:AD:DP:GQ:PL	0/1:3,17:20:16:521,0,16
-21	10200751	.	T	C	469.93	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=12.041;MLEAC=2;MLEAF=1.00;MQ=29.02;MQRankSum=1.52;QD=29.37;ReadPosRankSum=1.52;SOR=5.546	GT:AD:DP:GQ:PL	1/1:1,15:16:18:484,18,0
-21	10200881	.	T	C	681.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.883e+00;ClippingRankSum=1.75;DP=38;ExcessHet=3.0103;FS=4.815;MLEAC=1;MLEAF=0.500;MQ=28.73;MQRankSum=-9.050e-01;QD=17.94;ReadPosRankSum=-3.500e-01;SOR=1.164	GT:AD:DP:GQ:PL	0/1:19,19:38:99:689,0,479
-21	10200882	.	G	A	110.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.602;ClippingRankSum=0.715;DP=38;ExcessHet=3.0103;FS=20.623;MLEAC=1;MLEAF=0.500;MQ=28.73;MQRankSum=1.66;QD=2.91;ReadPosRankSum=-9.410e-01;SOR=4.167	GT:AD:DP:GQ:PL	0/1:31,7:38:99:118,0,1176
-21	10200902	.	T	C	220.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;ClippingRankSum=-3.800e-01;DP=44;ExcessHet=3.0103;FS=23.084;MLEAC=1;MLEAF=0.500;MQ=29.47;MQRankSum=-2.723e+00;QD=5.01;ReadPosRankSum=2.45;SOR=2.786	GT:AD:DP:GQ:PL	0/1:36,8:44:99:228,0,1488
-21	10200903	.	G	A	211.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;ClippingRankSum=1.84;DP=44;ExcessHet=3.0103;FS=23.084;MLEAC=1;MLEAF=0.500;MQ=29.47;MQRankSum=-2.693e+00;QD=4.81;ReadPosRankSum=2.48;SOR=2.786	GT:AD:DP:GQ:PL	0/1:36,8:44:99:219,0,1605
-21	10200908	.	C	A	330.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.644;ClippingRankSum=-8.230e-01;DP=52;ExcessHet=3.0103;FS=15.632;MLEAC=1;MLEAF=0.500;MQ=31.23;MQRankSum=0.287;QD=6.36;ReadPosRankSum=-6.050e-01;SOR=3.056	GT:AD:DP:GQ:PL	0/1:36,16:52:99:338,0,1230
-21	10200922	.	C	A	243.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-1.450e-01;DP=70;ExcessHet=3.0103;FS=20.227;MLEAC=1;MLEAF=0.500;MQ=30.72;MQRankSum=-2.840e+00;QD=3.48;ReadPosRankSum=0.113;SOR=0.974	GT:AD:DP:GQ:PL	0/1:59,11:70:99:251,0,2183
-21	10200955	.	A	G	466.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.470e+00;ClippingRankSum=1.40;DP=81;ExcessHet=3.0103;FS=4.748;MLEAC=1;MLEAF=0.500;MQ=31.86;MQRankSum=-1.085e+00;QD=5.76;ReadPosRankSum=0.165;SOR=1.487	GT:AD:DP:GQ:PL	0/1:63,18:81:99:474,0,2525
-21	10200961	.	G	A	1164.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.53;ClippingRankSum=0.793;DP=78;ExcessHet=3.0103;FS=20.991;MLEAC=1;MLEAF=0.500;MQ=32.49;MQRankSum=-3.125e+00;QD=15.12;ReadPosRankSum=0.639;SOR=3.366	GT:AD:DP:GQ:PL	0/1:42,35:77:99:1172,0,1190
-21	10200976	.	A	G	318.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.963e+00;ClippingRankSum=0.938;DP=82;ExcessHet=3.0103;FS=12.350;MLEAC=1;MLEAF=0.500;MQ=32.82;MQRankSum=-8.690e-01;QD=3.89;ReadPosRankSum=1.42;SOR=2.645	GT:AD:DP:GQ:PL	0/1:65,17:82:99:326,0,2261
-21	10200977	.	G	A	541.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;ClippingRankSum=0.028;DP=81;ExcessHet=3.0103;FS=14.979;MLEAC=1;MLEAF=0.500;MQ=32.86;MQRankSum=-3.416e+00;QD=6.69;ReadPosRankSum=0.162;SOR=2.978	GT:AD:DP:GQ:PL	0/1:62,19:81:99:549,0,2492
-21	10201009	.	A	C	1252.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165e+00;ClippingRankSum=-2.003e+00;DP=74;ExcessHet=3.0103;FS=106.234;MLEAC=1;MLEAF=0.500;MQ=31.54;MQRankSum=-5.229e+00;QD=16.93;ReadPosRankSum=-2.923e+00;SOR=7.378	GT:AD:DP:GQ:PL	0/1:35,39:74:99:1260,0,1280
-21	10201024	.	C	T	595.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.56;ClippingRankSum=0.566;DP=52;ExcessHet=3.0103;FS=55.697;MLEAC=1;MLEAF=0.500;MQ=32.43;MQRankSum=-2.965e+00;QD=11.45;ReadPosRankSum=-1.600e+00;SOR=5.782	GT:AD:DP:GQ:PL	0/1:35,17:52:99:603,0,1456
-21	10201028	.	T	C	1838.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.56;QD=30.67;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,48:48:99:1852,150,0
+21	10191583	.	G	A	100.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.190e-01;ClippingRankSum=-2.120e-01;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.26;MQRankSum=1.63;QD=7.19;ReadPosRankSum=0.495;SOR=0.412	GT:AD:DP:GQ:PL	0/1:10,4:14:99:108,0,264
+21	10192215	.	G	C	271.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.76;ClippingRankSum=1.05;DP=61;ExcessHet=3.0103;FS=4.151;MLEAC=1;MLEAF=0.500;MQ=26.83;MQRankSum=-2.490e-01;QD=4.45;ReadPosRankSum=-9.570e-01;SOR=1.461	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,17:61:99:0|1:10192215_G_C:279,0,1223
+21	10192716	.	T	C	117.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.525e+00;ClippingRankSum=-1.250e-01;DP=32;ExcessHet=3.0103;FS=39.428;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=1.58;QD=3.79;ReadPosRankSum=0.575;SOR=3.892	GT:AD:DP:GQ:PL	0/1:25,6:31:99:125,0,574
+21	10192752	.	T	C	92.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.119e+00;ClippingRankSum=-4.800e-01;DP=28;ExcessHet=3.0103;FS=23.278;MLEAC=1;MLEAF=0.500;MQ=23.24;MQRankSum=0.900;QD=3.31;ReadPosRankSum=2.22;SOR=3.588	GT:AD:DP:GQ:PL	0/1:23,5:28:99:100,0,532
+21	10193671	.	C	T	186.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.61;ClippingRankSum=0.606;DP=26;ExcessHet=3.0103;FS=7.204;MLEAC=1;MLEAF=0.500;MQ=24.20;MQRankSum=-8.700e-01;QD=7.18;ReadPosRankSum=0.501;SOR=2.409	GT:AD:DP:GQ:PL	0/1:16,10:26:99:194,0,467
+21	10193672	.	G	C	108.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=-2.890e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.12;MQRankSum=0.636;QD=4.18;ReadPosRankSum=-9.830e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:19,7:26:99:116,0,601
+21	10194878	.	C	T	97.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.396;ClippingRankSum=-5.780e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.62;MQRankSum=0.335;QD=4.07;ReadPosRankSum=1.73;SOR=0.646	GT:AD:DP:GQ:PL	0/1:20,4:26:99:105,0,983
+21	10194880	.	C	T	140.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.07;ClippingRankSum=-5.450e-01;DP=28;ExcessHet=3.0103;FS=2.276;MLEAC=1;MLEAF=0.500;MQ=31.62;MQRankSum=-1.524e+00;QD=10.82;ReadPosRankSum=-5.450e-01;SOR=1.535	GT:AD:DP:GQ:PL	0/1:7,6:14:99:148,0,706
+21	10196002	.	G	C	164.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.513e+00;ClippingRankSum=0.804;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.33;MQRankSum=0.910;QD=1.51;ReadPosRankSum=0.567;SOR=0.042	GT:AD:DP:GQ:PL	0/1:91,18:109:99:172,0,2263
+21	10196308	.	C	CA	1064.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.600e-01;ClippingRankSum=2.37;DP=328;ExcessHet=3.0103;FS=7.872;MLEAC=1;MLEAF=0.500;MQ=23.74;MQRankSum=1.59;QD=3.55;ReadPosRankSum=2.23;SOR=0.491	GT:AD:DP:GQ:PL	0/1:244,56:328:99:1072,0,6831
+21	10196317	.	A	G	173.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.982e+00;ClippingRankSum=0.314;DP=352;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.73;MQRankSum=0.737;QD=0.49;ReadPosRankSum=1.23;SOR=0.705	GT:AD:DP:GQ:PL	0/1:320,32:352:99:181,0,13193
+21	10196318	.	G	A	343.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.68;ClippingRankSum=0.197;DP=352;ExcessHet=3.0103;FS=0.630;MLEAC=1;MLEAF=0.500;MQ=23.73;MQRankSum=0.674;QD=1.00;ReadPosRankSum=1.66;SOR=0.608	GT:AD:DP:GQ:PL	0/1:313,32:352:99:351,0,12992
+21	10196368	.	G	GT	1337.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.830e-01;ClippingRankSum=1.58;DP=206;ExcessHet=3.0103;FS=4.452;MLEAC=1;MLEAF=0.500;MQ=23.66;MQRankSum=-2.712e+00;QD=10.53;ReadPosRankSum=-4.740e-01;SOR=0.399	GT:AD:DP:GQ:PL	0/1:76,51:138:99:1345,0,1733
+21	10196397	.	T	C	73.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.487e+00;ClippingRankSum=0.934;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.60;MQRankSum=0.102;QD=1.15;ReadPosRankSum=0.453;SOR=0.791	GT:AD:DP:GQ:PL	0/1:54,10:64:81:81,0,1360
+21	10196559	.	G	A	95.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.472;ClippingRankSum=0.766;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.09;MQRankSum=-1.150e-01;QD=1.68;ReadPosRankSum=2.63;SOR=0.051	GT:AD:DP:GQ:PL	0/1:47,10:57:99:103,0,1138
+21	10199880	.	A	AACAAACATTCAGACCACAGCAGGAGTGTTCTGGAATCCTATGTGAGG	160.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.960e-01;ClippingRankSum=0.087;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.10;MQRankSum=-5.630e-01;QD=2.01;ReadPosRankSum=-1.689e+00;SOR=1.270	GT:AD:DP:GQ:PL	0/1:79,1:80:99:168,0,3693
+21	10200470	.	G	T	73.14	.	AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.79;QD=18.29;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,4:4:12:87,12,0
+21	10200543	.	C	A	98.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;ClippingRankSum=-1.113e+00;DP=22;ExcessHet=3.0103;FS=7.929;MLEAC=1;MLEAF=0.500;MQ=23.00;MQRankSum=-1.361e+00;QD=4.93;ReadPosRankSum=-1.938e+00;SOR=1.093	GT:AD:DP:GQ:PL	0/1:14,6:20:99:106,0,328
+21	10200735	.	T	A	513.65	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.59;ClippingRankSum=1.16;DP=21;ExcessHet=3.0103;FS=18.016;MLEAC=1;MLEAF=0.500;MQ=28.99;MQRankSum=0.953;QD=25.68;ReadPosRankSum=0.423;SOR=5.782	GT:AD:DP:GQ:PL	0/1:3,17:20:16:521,0,16
+21	10200751	.	T	C	469.97	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=12.041;MLEAC=2;MLEAF=1.00;MQ=29.02;MQRankSum=1.52;QD=29.37;ReadPosRankSum=1.52;SOR=5.546	GT:AD:DP:GQ:PL	1/1:1,15:16:18:484,18,0
+21	10200881	.	T	C	681.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.883e+00;ClippingRankSum=1.75;DP=38;ExcessHet=3.0103;FS=4.815;MLEAC=1;MLEAF=0.500;MQ=28.73;MQRankSum=-9.050e-01;QD=17.94;ReadPosRankSum=-3.500e-01;SOR=1.164	GT:AD:DP:GQ:PL	0/1:19,19:38:99:689,0,479
+21	10200882	.	G	A	110.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.602;ClippingRankSum=0.715;DP=38;ExcessHet=3.0103;FS=20.623;MLEAC=1;MLEAF=0.500;MQ=28.73;MQRankSum=1.66;QD=2.91;ReadPosRankSum=-9.410e-01;SOR=4.167	GT:AD:DP:GQ:PL	0/1:31,7:38:99:118,0,1176
+21	10200902	.	T	C	220.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;ClippingRankSum=-3.800e-01;DP=44;ExcessHet=3.0103;FS=23.084;MLEAC=1;MLEAF=0.500;MQ=29.47;MQRankSum=-2.723e+00;QD=5.01;ReadPosRankSum=2.45;SOR=2.786	GT:AD:DP:GQ:PL	0/1:36,8:44:99:228,0,1488
+21	10200903	.	G	A	211.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;ClippingRankSum=1.84;DP=44;ExcessHet=3.0103;FS=23.084;MLEAC=1;MLEAF=0.500;MQ=29.47;MQRankSum=-2.693e+00;QD=4.81;ReadPosRankSum=2.48;SOR=2.786	GT:AD:DP:GQ:PL	0/1:36,8:44:99:219,0,1605
+21	10200908	.	C	A	330.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.644;ClippingRankSum=-8.230e-01;DP=52;ExcessHet=3.0103;FS=15.632;MLEAC=1;MLEAF=0.500;MQ=31.23;MQRankSum=0.287;QD=6.36;ReadPosRankSum=-6.050e-01;SOR=3.056	GT:AD:DP:GQ:PL	0/1:36,16:52:99:338,0,1230
+21	10200922	.	C	A	243.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-1.450e-01;DP=70;ExcessHet=3.0103;FS=20.227;MLEAC=1;MLEAF=0.500;MQ=30.72;MQRankSum=-2.840e+00;QD=3.48;ReadPosRankSum=0.113;SOR=0.974	GT:AD:DP:GQ:PL	0/1:59,11:70:99:251,0,2183
+21	10200955	.	A	G	466.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.470e+00;ClippingRankSum=1.40;DP=81;ExcessHet=3.0103;FS=4.748;MLEAC=1;MLEAF=0.500;MQ=31.86;MQRankSum=-1.085e+00;QD=5.76;ReadPosRankSum=0.165;SOR=1.487	GT:AD:DP:GQ:PL	0/1:63,18:81:99:474,0,2525
+21	10200961	.	G	A	1164.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.53;ClippingRankSum=0.793;DP=78;ExcessHet=3.0103;FS=20.991;MLEAC=1;MLEAF=0.500;MQ=32.49;MQRankSum=-3.125e+00;QD=15.13;ReadPosRankSum=0.639;SOR=3.366	GT:AD:DP:GQ:PL	0/1:42,35:77:99:1172,0,1190
+21	10200976	.	A	G	318.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.963e+00;ClippingRankSum=0.938;DP=82;ExcessHet=3.0103;FS=12.350;MLEAC=1;MLEAF=0.500;MQ=32.82;MQRankSum=-8.690e-01;QD=3.89;ReadPosRankSum=1.42;SOR=2.645	GT:AD:DP:GQ:PL	0/1:65,17:82:99:326,0,2261
+21	10200977	.	G	A	541.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;ClippingRankSum=0.028;DP=81;ExcessHet=3.0103;FS=14.979;MLEAC=1;MLEAF=0.500;MQ=32.86;MQRankSum=-3.416e+00;QD=6.69;ReadPosRankSum=0.162;SOR=2.978	GT:AD:DP:GQ:PL	0/1:62,19:81:99:549,0,2492
+21	10201009	.	A	C	1252.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165e+00;ClippingRankSum=-2.003e+00;DP=74;ExcessHet=3.0103;FS=106.234;MLEAC=1;MLEAF=0.500;MQ=31.54;MQRankSum=-5.229e+00;QD=16.93;ReadPosRankSum=-2.923e+00;SOR=7.378	GT:AD:DP:GQ:PL	0/1:35,39:74:99:1260,0,1280
+21	10201024	.	C	T	595.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.56;ClippingRankSum=0.566;DP=52;ExcessHet=3.0103;FS=55.697;MLEAC=1;MLEAF=0.500;MQ=32.43;MQRankSum=-2.965e+00;QD=11.45;ReadPosRankSum=-1.600e+00;SOR=5.782	GT:AD:DP:GQ:PL	0/1:35,17:52:99:603,0,1456
+21	10201028	.	T	C	1838.06	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.56;QD=30.67;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,48:48:99:1852,150,0
 21	10201032	.	CTATGTCCTTACTGA	C	130.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.240e-01;ClippingRankSum=-1.580e-01;DP=46;ExcessHet=3.0103;FS=23.516;MLEAC=1;MLEAF=0.500;MQ=32.60;MQRankSum=-2.716e+00;QD=3.04;ReadPosRankSum=0.123;SOR=3.898	GT:AD:DP:GQ:PL	0/1:37,6:43:99:138,0,1577
-21	10201033	.	T	C	87.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.648e+00;ClippingRankSum=0.170;DP=46;ExcessHet=3.0103;FS=19.179;MLEAC=1;MLEAF=0.500;MQ=32.60;MQRankSum=-2.444e+00;QD=2.04;ReadPosRankSum=2.97;SOR=3.593	GT:AD:DP:GQ:PL	0/1:38,5:43:95:95,0,1581
-21	10201035	.	T	A	87.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.322;DP=46;ExcessHet=3.0103;FS=19.179;MLEAC=1;MLEAF=0.500;MQ=32.60;MQRankSum=-2.330e+00;QD=2.04;ReadPosRankSum=2.75;SOR=3.593	GT:AD:DP:GQ:PL	0/1:38,5:43:95:95,0,1581
-21	10201190	.	T	C	652.03	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.04;QD=26.61;SOR=2.712	GT:AD:DP:GQ:PL	1/1:0,17:17:51:666,51,0
-21	10201200	.	T	A	544.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=0.206;DP=33;ExcessHet=3.0103;FS=3.267;MLEAC=1;MLEAF=0.500;MQ=30.80;MQRankSum=-1.329e+00;QD=16.50;ReadPosRankSum=0.767;SOR=1.371	GT:AD:DP:GQ:PL	0/1:12,21:33:99:552,0,262
-21	10201228	.	T	C	507.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.569e+00;ClippingRankSum=-8.360e-01;DP=86;ExcessHet=3.0103;FS=0.945;MLEAC=1;MLEAF=0.500;MQ=33.29;MQRankSum=-3.500e-02;QD=5.90;ReadPosRankSum=-2.030e-01;SOR=0.931	GT:AD:DP:GQ:PL	0/1:64,22:86:99:515,0,2077
-21	10201298	.	G	C	593.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.70;ClippingRankSum=0.651;DP=202;ExcessHet=3.0103;FS=4.304;MLEAC=1;MLEAF=0.500;MQ=32.45;MQRankSum=-2.770e+00;QD=2.94;ReadPosRankSum=1.96;SOR=1.060	GT:AD:DP:GQ:PL	0/1:164,38:202:99:601,0,5489
-21	10201317	.	T	G	496.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.595e+00;ClippingRankSum=-2.190e-01;DP=169;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.71;MQRankSum=2.13;QD=2.94;ReadPosRankSum=-2.474e+00;SOR=0.627	GT:AD:DP:GQ:PL	0/1:137,32:169:99:504,0,4767
-21	10201343	.	C	A	561.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;ClippingRankSum=0.411;DP=106;ExcessHet=3.0103;FS=8.622;MLEAC=1;MLEAF=0.500;MQ=30.76;MQRankSum=-2.190e+00;QD=5.30;ReadPosRankSum=-4.300e-02;SOR=0.197	GT:AD:DP:GQ:PL	0/1:77,29:106:99:569,0,3146
-21	10201361	.	C	T	718.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.22;ClippingRankSum=-1.110e-01;DP=56;ExcessHet=3.0103;FS=2.921;MLEAC=1;MLEAF=0.500;MQ=29.16;MQRankSum=1.96;QD=12.83;ReadPosRankSum=-1.154e+00;SOR=0.283	GT:AD:DP:GQ:PL	0/1:36,20:56:99:726,0,933
-21	10201514	.	A	G	346.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=-2.600e-02;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.80;MQRankSum=0.333;QD=8.25;ReadPosRankSum=1.26;SOR=0.551	GT:AD:DP:GQ:PL	0/1:25,17:42:99:354,0,568
-21	10201769	.	G	A	39.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.531e+00;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=7.404;MLEAC=1;MLEAF=0.500;MQ=20.56;MQRankSum=2.26;QD=3.60;ReadPosRankSum=2.26;SOR=2.800	GT:AD:DP:GQ:PL	0/1:8,3:11:47:47,0,165
-21	10202809	.	A	T	264.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.306;ClippingRankSum=0.703;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.00;MQRankSum=-7.030e-01;QD=7.78;ReadPosRankSum=-4.140e-01;SOR=0.892	GT:AD:DP:GQ:PL	0/1:22,12:34:99:272,0,613
-21	10202904	.	G	C	131.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.04;ClippingRankSum=-2.300e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.93;MQRankSum=0.265;QD=3.56;ReadPosRankSum=1.22;SOR=0.743	GT:AD:DP:GQ:PL	0/1:28,9:37:99:139,0,666
-21	10204134	.	C	A	749.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.880e-01;ClippingRankSum=-1.570e-01;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.91;MQRankSum=-4.557e+00;QD=12.49;ReadPosRankSum=0.559;SOR=0.676	GT:AD:DP:GQ:PL	0/1:26,34:60:99:757,0,816
-21	10204295	.	C	T	256.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.492;ClippingRankSum=0.680;DP=30;ExcessHet=3.0103;FS=20.288;MLEAC=1;MLEAF=0.500;MQ=24.01;MQRankSum=-2.300e-02;QD=8.55;ReadPosRankSum=-2.603e+00;SOR=2.783	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,8:30:99:1|0:10204290_G_C:264,0,1097
-21	10204303	.	G	A	250.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;ClippingRankSum=-2.230e-01;DP=34;ExcessHet=3.0103;FS=24.039;MLEAC=1;MLEAF=0.500;MQ=25.72;MQRankSum=-8.730e-01;QD=7.37;ReadPosRankSum=-1.482e+00;SOR=2.783	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,8:34:99:1|0:10204290_G_C:258,0,1160
-21	10204627	.	G	C	59.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176e+00;ClippingRankSum=-5.090e-01;DP=19;ExcessHet=3.0103;FS=2.754;MLEAC=1;MLEAF=0.500;MQ=20.34;MQRankSum=-6.940e-01;QD=3.14;ReadPosRankSum=-5.090e-01;SOR=2.133	GT:AD:DP:GQ:PL	0/1:14,5:19:67:67,0,295
-21	10205589	.	G	A	208.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.684e+00;ClippingRankSum=0.521;DP=24;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=37.00;MQRankSum=-1.010e+00;QD=8.69;ReadPosRankSum=-1.439e+00;SOR=1.179	GT:AD:DP:GQ:PL	0/1:16,8:24:99:216,0,507
-21	10205629	.	A	G	214.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.787e+00;ClippingRankSum=-5.760e-01;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.33;MQRankSum=1.33;QD=5.37;ReadPosRankSum=1.18;SOR=0.536	GT:AD:DP:GQ:PL	0/1:29,11:40:99:222,0,861
-21	10208181	.	C	T	1442.03	.	AC=2;AF=1.00;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.81;QD=29.20;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,37:37:99:1456,111,0
-21	10208997	.	G	A	554.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;ClippingRankSum=-1.450e-01;DP=44;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.500;MQ=36.67;MQRankSum=-6.510e-01;QD=12.60;ReadPosRankSum=0.434;SOR=0.479	GT:AD:DP:GQ:PL	0/1:27,17:44:99:562,0,958
-21	10209579	.	G	C	151.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709e+00;ClippingRankSum=-1.591e+00;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.03;MQRankSum=-2.950e-01;QD=10.11;ReadPosRankSum=-1.002e+00;SOR=0.399	GT:AD:DP:GQ:PL	0/1:9,6:15:99:159,0,266
-21	10209968	.	C	A	1029.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;ClippingRankSum=0.052;DP=60;ExcessHet=3.0103;FS=2.325;MLEAC=1;MLEAF=0.500;MQ=37.42;MQRankSum=-4.960e-01;QD=17.16;ReadPosRankSum=1.00;SOR=0.392	GT:AD:DP:GQ:PL	0/1:28,32:60:99:1037,0,862
-21	10210279	.	T	C	367.02	.	AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=30.59;SOR=5.136	GT:AD:DP:GQ:PL	1/1:0,12:12:36:381,36,0
-21	10211731	.	C	T	216.93	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.75;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,6:6:18:231,18,0
-21	10211989	.	C	T	62.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.860e-01;ClippingRankSum=0.634;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.69;MQRankSum=-1.528e+00;QD=2.72;ReadPosRankSum=-1.081e+00;SOR=0.095	GT:AD:DP:GQ:PL	0/1:18,5:23:70:70,0,430
-21	10212117	.	C	T	61.61	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-7.270e-01;DP=5;ExcessHet=3.0103;FS=6.021;MLEAC=1;MLEAF=0.500;MQ=26.96;MQRankSum=-7.270e-01;QD=15.40;ReadPosRankSum=0.727;SOR=2.788	GT:AD:DP:GQ:PL	0/1:1,3:4:20:69,0,20
-21	10212330	.	G	A	263.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.01;ClippingRankSum=2.94;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.35;MQRankSum=2.47;QD=18.83;ReadPosRankSum=2.80;SOR=1.179	GT:AD:DP:GQ:PL	0/1:6,8:14:99:271,0,129
-21	10212343	.	A	G	123.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.680e-01;ClippingRankSum=-1.740e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.76;MQRankSum=-2.720e+00;QD=8.24;ReadPosRankSum=-2.488e+00;SOR=0.527	GT:AD:DP:GQ:PL	0/1:8,7:15:99:131,0,248
+21	10201033	.	T	C	87.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.648e+00;ClippingRankSum=0.170;DP=46;ExcessHet=3.0103;FS=19.179;MLEAC=1;MLEAF=0.500;MQ=32.60;MQRankSum=-2.444e+00;QD=2.04;ReadPosRankSum=2.97;SOR=3.593	GT:AD:DP:GQ:PL	0/1:38,5:43:95:95,0,1581
+21	10201035	.	T	A	87.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.322;DP=46;ExcessHet=3.0103;FS=19.179;MLEAC=1;MLEAF=0.500;MQ=32.60;MQRankSum=-2.330e+00;QD=2.04;ReadPosRankSum=2.75;SOR=3.593	GT:AD:DP:GQ:PL	0/1:38,5:43:95:95,0,1581
+21	10201190	.	T	C	652.06	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.04;QD=26.61;SOR=2.712	GT:AD:DP:GQ:PL	1/1:0,17:17:51:666,51,0
+21	10201200	.	T	A	544.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=0.206;DP=33;ExcessHet=3.0103;FS=3.267;MLEAC=1;MLEAF=0.500;MQ=30.80;MQRankSum=-1.329e+00;QD=16.50;ReadPosRankSum=0.767;SOR=1.371	GT:AD:DP:GQ:PL	0/1:12,21:33:99:552,0,262
+21	10201228	.	T	C	507.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.569e+00;ClippingRankSum=-8.360e-01;DP=86;ExcessHet=3.0103;FS=0.945;MLEAC=1;MLEAF=0.500;MQ=33.29;MQRankSum=-3.500e-02;QD=5.90;ReadPosRankSum=-2.030e-01;SOR=0.931	GT:AD:DP:GQ:PL	0/1:64,22:86:99:515,0,2077
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+21	10201317	.	T	G	496.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.595e+00;ClippingRankSum=-2.190e-01;DP=169;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.71;MQRankSum=2.13;QD=2.94;ReadPosRankSum=-2.474e+00;SOR=0.627	GT:AD:DP:GQ:PL	0/1:137,32:169:99:504,0,4767
+21	10201343	.	C	A	561.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;ClippingRankSum=0.411;DP=106;ExcessHet=3.0103;FS=8.622;MLEAC=1;MLEAF=0.500;MQ=30.76;MQRankSum=-2.190e+00;QD=5.30;ReadPosRankSum=-4.300e-02;SOR=0.197	GT:AD:DP:GQ:PL	0/1:77,29:106:99:569,0,3146
+21	10201361	.	C	T	718.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.22;ClippingRankSum=-1.110e-01;DP=56;ExcessHet=3.0103;FS=2.921;MLEAC=1;MLEAF=0.500;MQ=29.16;MQRankSum=1.96;QD=12.83;ReadPosRankSum=-1.154e+00;SOR=0.283	GT:AD:DP:GQ:PL	0/1:36,20:56:99:726,0,933
+21	10201514	.	A	G	346.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=-2.600e-02;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.80;MQRankSum=0.333;QD=8.25;ReadPosRankSum=1.26;SOR=0.551	GT:AD:DP:GQ:PL	0/1:25,17:42:99:354,0,568
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+21	10202809	.	A	T	264.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.306;ClippingRankSum=0.703;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.00;MQRankSum=-7.030e-01;QD=7.78;ReadPosRankSum=-4.140e-01;SOR=0.892	GT:AD:DP:GQ:PL	0/1:22,12:34:99:272,0,613
+21	10202904	.	G	C	131.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.04;ClippingRankSum=-2.300e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.93;MQRankSum=0.265;QD=3.56;ReadPosRankSum=1.22;SOR=0.743	GT:AD:DP:GQ:PL	0/1:28,9:37:99:139,0,666
+21	10204134	.	C	A	749.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.880e-01;ClippingRankSum=-1.570e-01;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.91;MQRankSum=-4.557e+00;QD=12.49;ReadPosRankSum=0.559;SOR=0.676	GT:AD:DP:GQ:PL	0/1:26,34:60:99:757,0,816
+21	10204295	.	C	T	256.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.492;ClippingRankSum=0.680;DP=30;ExcessHet=3.0103;FS=20.288;MLEAC=1;MLEAF=0.500;MQ=24.01;MQRankSum=-2.300e-02;QD=8.55;ReadPosRankSum=-2.603e+00;SOR=2.783	GT:AD:DP:GQ:PGT:PID:PL	0/1:22,8:30:99:1|0:10204290_G_C:264,0,1097
+21	10204303	.	G	A	250.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;ClippingRankSum=-2.230e-01;DP=34;ExcessHet=3.0103;FS=24.039;MLEAC=1;MLEAF=0.500;MQ=25.72;MQRankSum=-8.730e-01;QD=7.37;ReadPosRankSum=-1.482e+00;SOR=2.783	GT:AD:DP:GQ:PGT:PID:PL	0/1:26,8:34:99:1|0:10204290_G_C:258,0,1160
+21	10204627	.	G	C	59.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176e+00;ClippingRankSum=-5.090e-01;DP=19;ExcessHet=3.0103;FS=2.754;MLEAC=1;MLEAF=0.500;MQ=20.34;MQRankSum=-6.940e-01;QD=3.14;ReadPosRankSum=-5.090e-01;SOR=2.133	GT:AD:DP:GQ:PL	0/1:14,5:19:67:67,0,295
+21	10205589	.	G	A	208.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.684e+00;ClippingRankSum=0.521;DP=24;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=37.00;MQRankSum=-1.010e+00;QD=8.69;ReadPosRankSum=-1.439e+00;SOR=1.179	GT:AD:DP:GQ:PL	0/1:16,8:24:99:216,0,507
+21	10205629	.	A	G	214.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.787e+00;ClippingRankSum=-5.760e-01;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.33;MQRankSum=1.33;QD=5.37;ReadPosRankSum=1.18;SOR=0.536	GT:AD:DP:GQ:PL	0/1:29,11:40:99:222,0,861
+21	10208181	.	C	T	1442.06	.	AC=2;AF=1.00;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.81;QD=29.20;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,37:37:99:1456,111,0
+21	10208997	.	G	A	554.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;ClippingRankSum=-1.450e-01;DP=44;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.500;MQ=36.67;MQRankSum=-6.510e-01;QD=12.61;ReadPosRankSum=0.434;SOR=0.479	GT:AD:DP:GQ:PL	0/1:27,17:44:99:562,0,958
+21	10209579	.	G	C	151.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709e+00;ClippingRankSum=-1.591e+00;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.03;MQRankSum=-2.950e-01;QD=10.11;ReadPosRankSum=-1.002e+00;SOR=0.399	GT:AD:DP:GQ:PL	0/1:9,6:15:99:159,0,266
+21	10209968	.	C	A	1029.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;ClippingRankSum=0.052;DP=60;ExcessHet=3.0103;FS=2.325;MLEAC=1;MLEAF=0.500;MQ=37.42;MQRankSum=-4.960e-01;QD=17.16;ReadPosRankSum=1.00;SOR=0.392	GT:AD:DP:GQ:PL	0/1:28,32:60:99:1037,0,862
+21	10210279	.	T	C	367.06	.	AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;QD=30.59;SOR=5.136	GT:AD:DP:GQ:PL	1/1:0,12:12:36:381,36,0
+21	10211731	.	C	T	216.97	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.75;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,6:6:18:231,18,0
+21	10211989	.	C	T	62.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.860e-01;ClippingRankSum=0.634;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.69;MQRankSum=-1.528e+00;QD=2.72;ReadPosRankSum=-1.081e+00;SOR=0.095	GT:AD:DP:GQ:PL	0/1:18,5:23:70:70,0,430
+21	10212117	.	C	T	61.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-7.270e-01;DP=5;ExcessHet=3.0103;FS=6.021;MLEAC=1;MLEAF=0.500;MQ=26.96;MQRankSum=-7.270e-01;QD=15.41;ReadPosRankSum=0.727;SOR=2.788	GT:AD:DP:GQ:PL	0/1:1,3:4:20:69,0,20
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+21	10212343	.	A	G	123.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.680e-01;ClippingRankSum=-1.740e-01;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.76;MQRankSum=-2.720e+00;QD=8.24;ReadPosRankSum=-2.488e+00;SOR=0.527	GT:AD:DP:GQ:PL	0/1:8,7:15:99:131,0,248
 21	10212396	.	GAA	G	256.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.480e-01;ClippingRankSum=-1.160e-01;DP=40;ExcessHet=3.0103;FS=5.329;MLEAC=1;MLEAF=0.500;MQ=28.13;MQRankSum=4.43;QD=6.75;ReadPosRankSum=-2.735e+00;SOR=0.877	GT:AD:DP:GQ:PL	0/1:28,10:38:99:264,0,964
-21	10212444	.	A	G	348.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.338e+00;ClippingRankSum=-1.719e+00;DP=50;ExcessHet=3.0103;FS=5.936;MLEAC=1;MLEAF=0.500;MQ=25.19;MQRankSum=-4.400e-01;QD=6.97;ReadPosRankSum=3.16;SOR=1.204	GT:AD:DP:GQ:PL	0/1:31,19:50:99:356,0,773
-21	10213845	.	A	G	251.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.380e+00;ClippingRankSum=-4.830e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.11;MQRankSum=0.612;QD=6.62;ReadPosRankSum=-1.159e+00;SOR=0.169	GT:AD:DP:GQ:PL	0/1:27,11:38:99:259,0,781
-21	10213876	.	C	T	30.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.19;ClippingRankSum=0.275;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.79;MQRankSum=-3.970e-01;QD=1.02;ReadPosRankSum=-6.410e-01;SOR=0.034	GT:AD:DP:GQ:PL	0/1:26,4:30:38:38,0,776
-21	10214079	.	C	T	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.486e+00;ClippingRankSum=-1.100e-01;DP=30;ExcessHet=3.0103;FS=17.593;MLEAC=1;MLEAF=0.500;MQ=31.65;MQRankSum=-2.618e+00;QD=2.25;ReadPosRankSum=0.638;SOR=3.238	GT:AD:DP:GQ:PL	0/1:20,10:30:75:75,0,553
-21	10214130	.	C	CA	558.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;ClippingRankSum=-4.700e-02;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.07;MQRankSum=-7.160e-01;QD=6.35;ReadPosRankSum=1.08;SOR=0.669	GT:AD:DP:GQ:PL	0/1:54,34:88:99:566,0,1178
-21	10214390	.	G	C	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.500e-01;ClippingRankSum=0.150;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.49;MQRankSum=0.850;QD=3.56;ReadPosRankSum=-2.250e+00;SOR=0.368	GT:AD:DP:GQ:PL	0/1:15,4:19:75:75,0,407
+21	10212444	.	A	G	348.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.338e+00;ClippingRankSum=-1.719e+00;DP=50;ExcessHet=3.0103;FS=5.936;MLEAC=1;MLEAF=0.500;MQ=25.19;MQRankSum=-4.400e-01;QD=6.97;ReadPosRankSum=3.16;SOR=1.204	GT:AD:DP:GQ:PL	0/1:31,19:50:99:356,0,773
+21	10213845	.	A	G	251.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.380e+00;ClippingRankSum=-4.830e-01;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.11;MQRankSum=0.612;QD=6.62;ReadPosRankSum=-1.159e+00;SOR=0.169	GT:AD:DP:GQ:PL	0/1:27,11:38:99:259,0,781
+21	10213876	.	C	T	30.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.19;ClippingRankSum=0.275;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.79;MQRankSum=-3.970e-01;QD=1.02;ReadPosRankSum=-6.410e-01;SOR=0.034	GT:AD:DP:GQ:PL	0/1:26,4:30:38:38,0,776
+21	10214079	.	C	T	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.486e+00;ClippingRankSum=-1.100e-01;DP=30;ExcessHet=3.0103;FS=17.593;MLEAC=1;MLEAF=0.500;MQ=31.65;MQRankSum=-2.618e+00;QD=2.25;ReadPosRankSum=0.638;SOR=3.238	GT:AD:DP:GQ:PL	0/1:20,10:30:75:75,0,553
+21	10214130	.	C	CA	558.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;ClippingRankSum=-4.700e-02;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.07;MQRankSum=-7.160e-01;QD=6.35;ReadPosRankSum=1.08;SOR=0.669	GT:AD:DP:GQ:PL	0/1:54,34:88:99:566,0,1178
+21	10214390	.	G	C	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.500e-01;ClippingRankSum=0.150;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.49;MQRankSum=0.850;QD=3.56;ReadPosRankSum=-2.250e+00;SOR=0.368	GT:AD:DP:GQ:PL	0/1:15,4:19:75:75,0,407
 21	10214733	.	TGTAAAAATTTGAAATCATAATTATGCTA	T	184.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.143;ClippingRankSum=1.19;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.31;MQRankSum=0.143;QD=16.78;ReadPosRankSum=-1.652e+00;SOR=0.551	GT:AD:DP:GQ:PL	0/1:6,5:11:99:192,0,237
-21	10214800	.	C	T	49.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.170e-01;ClippingRankSum=0.217;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.68;MQRankSum=-2.170e-01;QD=3.31;ReadPosRankSum=0.650;SOR=0.090	GT:AD:DP:GQ:PL	0/1:12,3:15:57:57,0,361
-21	10214811	.	C	T	509.03	.	AC=2;AF=1.00;AN=2;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.64;QD=33.94;SOR=5.549	GT:AD:DP:GQ:PL	1/1:0,15:15:45:523,45,0
-21	10214917	.	T	G	51.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQRankSum=0.736;QD=17.20;ReadPosRankSum=-7.360e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:1,2:3:25:59,0,25
-21	10215006	.	A	AT	227.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.386;ClippingRankSum=0.386;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-5.400e-01;QD=17.51;ReadPosRankSum=0.231;SOR=0.569	GT:AD:DP:GQ:PL	0/1:4,9:13:83:235,0,83
-21	10215083	.	A	C	367.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.100e-02;ClippingRankSum=-1.115e+00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.70;MQRankSum=0.537;QD=19.35;ReadPosRankSum=3.59;SOR=0.859	GT:AD:DP:GQ:PL	0/1:8,11:19:99:375,0,212
-21	10215085	.	A	C	166.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.170e-01;ClippingRankSum=-1.194e+00;DP=25;ExcessHet=3.0103;FS=1.792;MLEAC=1;MLEAF=0.500;MQ=33.53;MQRankSum=0.580;QD=7.57;ReadPosRankSum=3.04;SOR=0.307	GT:AD:DP:GQ:PL	0/1:14,8:22:99:174,0,561
+21	10214800	.	C	T	49.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.170e-01;ClippingRankSum=0.217;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.68;MQRankSum=-2.170e-01;QD=3.31;ReadPosRankSum=0.650;SOR=0.090	GT:AD:DP:GQ:PL	0/1:12,3:15:57:57,0,361
+21	10214811	.	C	T	509.06	.	AC=2;AF=1.00;AN=2;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.64;QD=33.94;SOR=5.549	GT:AD:DP:GQ:PL	1/1:0,15:15:45:523,45,0
+21	10214917	.	T	G	51.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQRankSum=0.736;QD=17.21;ReadPosRankSum=-7.360e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:1,2:3:25:59,0,25
+21	10215006	.	A	AT	227.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.386;ClippingRankSum=0.386;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=-5.400e-01;QD=17.51;ReadPosRankSum=0.231;SOR=0.569	GT:AD:DP:GQ:PL	0/1:4,9:13:83:235,0,83
+21	10215083	.	A	C	367.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.100e-02;ClippingRankSum=-1.115e+00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.70;MQRankSum=0.537;QD=19.35;ReadPosRankSum=3.59;SOR=0.859	GT:AD:DP:GQ:PL	0/1:8,11:19:99:375,0,212
+21	10215085	.	A	C	166.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.170e-01;ClippingRankSum=-1.194e+00;DP=25;ExcessHet=3.0103;FS=1.792;MLEAC=1;MLEAF=0.500;MQ=33.53;MQRankSum=0.580;QD=7.57;ReadPosRankSum=3.04;SOR=0.307	GT:AD:DP:GQ:PL	0/1:14,8:22:99:174,0,561
 21	10215108	.	TA	T	128.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=-5.530e-01;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.75;MQRankSum=0.837;QD=2.86;ReadPosRankSum=1.35;SOR=0.892	GT:AD:DP:GQ:PL	0/1:36,9:45:99:136,0,1096
-21	10215182	.	C	G	694.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.349;ClippingRankSum=0.891;DP=24;ExcessHet=3.0103;FS=9.432;MLEAC=1;MLEAF=0.500;MQ=35.48;MQRankSum=-3.900e-02;QD=28.94;ReadPosRankSum=-9.680e-01;SOR=0.039	GT:AD:DP:GQ:PL	0/1:4,20:24:80:702,0,80
-21	10215376	.	A	C	42.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.572;ClippingRankSum=-1.067e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.12;MQRankSum=0.572;QD=5.33;ReadPosRankSum=-5.720e-01;SOR=0.169	GT:AD:DP:GQ:PL	0/1:6,2:8:50:50,0,170
+21	10215182	.	C	G	694.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.349;ClippingRankSum=0.891;DP=24;ExcessHet=3.0103;FS=9.432;MLEAC=1;MLEAF=0.500;MQ=35.48;MQRankSum=-3.900e-02;QD=28.94;ReadPosRankSum=-9.680e-01;SOR=0.039	GT:AD:DP:GQ:PL	0/1:4,20:24:80:702,0,80
+21	10215376	.	A	C	42.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.572;ClippingRankSum=-1.067e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.12;MQRankSum=0.572;QD=5.33;ReadPosRankSum=-5.720e-01;SOR=0.169	GT:AD:DP:GQ:PL	0/1:6,2:8:50:50,0,170
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ad-bug-gatk3.7_30_ga4f720357-output.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ad-bug-gatk3.7_30_ga4f720357-output.vcf
index bdcdfb02355..660611dc9ab 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ad-bug-gatk3.7_30_ga4f720357-output.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ad-bug-gatk3.7_30_ga4f720357-output.vcf
@@ -11,7 +11,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-48-g1b179dd,Date="Thu Jul 16 11:05:21 EDT 2015",Epoch=1437059121738,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[MT1to1000.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[MT] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ad-bug-gatk3.7_30_ga4f720357-output.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ad-bug-input.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:16 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -116,14 +115,13 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/gsa-hpprojects/GATK/bundle/2.8/b37/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	C3
-20	73	.	A	G	16524.01	.	AC=1;AF=1.00;AN=1;DP=446;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.19;QD=25.36;SOR=1.106	GT:AD:DP:GQ:PL	1:0,446:446:99:16534,0
-20	149	.	TCC	T	12410.04	.	AC=1;AF=1.00;AN=1;DP=304;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.67;QD=28.73;SOR=1.183	GT:AD:DP:GQ:PL	1:0,274:276:99:12420,0
-20	152	.	T	TTC	7354.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.014;ClippingRankSum=1.44;DP=273;FS=7.935;MLEAC=1;MLEAF=1.00;MQ=59.77;MQRankSum=0.629;QD=27.34;ReadPosRankSum=0.258;SOR=0.871	GT:AD:DP:GQ:PL	1:2,267:271:99:7364,0
-20	263	.	A	G	10098.01	.	AC=1;AF=1.00;AN=1;DP=261;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.97;SOR=1.250	GT:AD:DP:GQ:PL	1:0,261:261:99:10108,0
-20	295	.	C	T	5045.01	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.31;ClippingRankSum=0.751;DP=133;FS=13.148;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=-8.580e-01;QD=27.24;ReadPosRankSum=3.06;SOR=1.448	GT:AD:DP:GQ:PL	1:5,128:133:99:5055,0
-20	302	.	A	AC	4068.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.320e-01;ClippingRankSum=-4.400e-02;DP=109;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=-8.660e-01;QD=28.20;ReadPosRankSum=1.95;SOR=3.816	GT:AD:DP:GQ:PL	1:2,35:84:99:4078,0
-20	310	.	T	TC	3029.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.75;ClippingRankSum=-7.480e-01;DP=88;FS=27.847;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=1.10;QD=25.00;ReadPosRankSum=2.92;SOR=8.838	GT:AD:DP:GQ:PL	1:4,48:86:99:3039,0
-20	489	.	T	C	3132.01	.	AC=1;AF=1.00;AN=1;DP=92;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=34.04;SOR=7.658	GT:AD:DP:GQ:PL	1:0,92:92:99:3142,0
-20	750	.	A	G	13918.01	.	AC=1;AF=1.00;AN=1;DP=402;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.86;QD=34.62;SOR=1.449	GT:AD:DP:GQ:PL	1:0,402:402:99:13928,0
+20	73	.	A	G	16524.04	.	AC=1;AF=1.00;AN=1;DP=446;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.19;QD=25.36;SOR=1.106	GT:AD:DP:GQ:PL	1:0,446:446:99:16534,0
+20	149	.	TCC	T	12410.01	.	AC=1;AF=1.00;AN=1;DP=304;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.67;QD=28.73;SOR=1.183	GT:AD:DP:GQ:PL	1:0,274:276:99:12420,0
+20	152	.	T	TTC	7354.01	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.014;ClippingRankSum=1.44;DP=273;FS=7.935;MLEAC=1;MLEAF=1.00;MQ=59.77;MQRankSum=0.629;QD=27.34;ReadPosRankSum=0.258;SOR=0.871	GT:AD:DP:GQ:PL	1:2,267:271:99:7364,0
+20	263	.	A	G	10098.04	.	AC=1;AF=1.00;AN=1;DP=261;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.97;SOR=1.250	GT:AD:DP:GQ:PL	1:0,261:261:99:10108,0
+20	295	.	C	T	5045.04	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.31;ClippingRankSum=0.751;DP=133;FS=13.148;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=-8.580e-01;QD=27.24;ReadPosRankSum=3.06;SOR=1.448	GT:AD:DP:GQ:PL	1:5,128:133:99:5055,0
+20	302	.	A	AC	4068.01	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.320e-01;ClippingRankSum=-4.400e-02;DP=109;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=-8.660e-01;QD=28.20;ReadPosRankSum=1.95;SOR=3.816	GT:AD:DP:GQ:PL	1:2,35:84:99:4078,0
+20	310	.	T	TC	3029.01	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.75;ClippingRankSum=-7.480e-01;DP=88;FS=27.847;MLEAC=1;MLEAF=1.00;MQ=60.00;MQRankSum=1.10;QD=25.00;ReadPosRankSum=2.92;SOR=8.838	GT:AD:DP:GQ:PL	1:4,48:86:99:3039,0
+20	489	.	T	C	3132.04	.	AC=1;AF=1.00;AN=1;DP=92;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.99;QD=34.04;SOR=7.658	GT:AD:DP:GQ:PL	1:0,92:92:99:3142,0
+20	750	.	A	G	13918.04	.	AC=1;AF=1.00;AN=1;DP=402;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=59.86;QD=34.62;SOR=1.449	GT:AD:DP:GQ:PL	1:0,402:402:99:13928,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf
index 43b123449b8..a768e8882e4 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf1398129936360043648.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/chr21.bad.pl.g.vcf --intervals chr21:28341770-28341790 --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --input-is-somatic false --tumor-lod-to-emit 4.24 --allele-fraction-error 0.001 --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="February 22, 2019 12:17:17 PM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -3400,7 +3399,6 @@
 ##contig=<ID=HLA-DRB1*15:03:01:01,length=11567>
 ##contig=<ID=HLA-DRB1*15:03:01:02,length=11569>
 ##contig=<ID=HLA-DRB1*16:02:01,length=11005>
-##source=GenotypeGVCFs
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00268	HG00419	HG00759	HG01051	HG01112	HG01500	HG01565	HG01583	HG01595	HG01879	HG02568	HG02922	HG03006	HG03052	HG03642	HG03742	NA18525	NA18939	NA19017	NA19625	NA19648	NA20502	NA20845
-chr21	28341778	.	G	A	479.82	.	AC=1;AF=0.022;AN=46;BaseQRankSum=1.12;ClippingRankSum=0.329;DP=914;ExcessHet=3.0103;FS=6.865;InbreedingCoeff=0.1268;MLEAC=1;MLEAF=0.022;MQ=59.29;MQRankSum=0.152;QD=9.79;RAW_MQ=298800.00;ReadPosRankSum=-2.530e-01;SOR=0.236	GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,99,1210	0/0:44,0:44:99:0,105,1317	0/0:43,0:43:0:0,0,83	0/0:54,0:54:0:0,0,524	0/0:34,0:34:99:0,99,1061	0/0:44,0:44:99:0,107,1464	0/0:38,0:38:99:0,101,1138	0/0:32,0:34:94:0,94,831	0/0:40,0:40:99:0,103,1210	0/0:36,0:36:99:0,103,1055	0/0:39,0:39:99:0,104,1179	0/0:17,0:17:51:0,51,471	0/0:39,0:39:99:0,110,1170	0/0:35,0:35:99:0,105,1040	0/0:36,0:36:99:0,99,1030	0/0:32,0:32:0:0,0,266	0/0:43,0:43:99:0,100,1295	0/0:35,0:35:99:0,105,1071	0/0:34,0:34:99:0,99,1056	0/0:34,0:34:99:0,102,1031	./.:36,0:36:.:0,0,0	0/1:28,21:49:99:493,0,646	0/0:42,0:42:99:0,101,1499	0/0:41,0:41:99:0,103,1368
+chr21	28341778	.	G	A	479.87	.	AC=1;AF=0.022;AN=46;BaseQRankSum=1.12;ClippingRankSum=0.329;DP=914;ExcessHet=3.0103;FS=6.865;InbreedingCoeff=0.1268;MLEAC=1;MLEAF=0.022;MQ=59.29;MQRankSum=0.152;QD=9.79;RAW_MQ=298800.00;ReadPosRankSum=-2.530e-01;SOR=0.236	GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,99,1210	0/0:44,0:44:99:0,105,1317	0/0:43,0:43:0:0,0,83	0/0:54,0:54:0:0,0,524	0/0:34,0:34:99:0,99,1061	0/0:44,0:44:99:0,107,1464	0/0:38,0:38:99:0,101,1138	0/0:32,0:34:94:0,94,831	0/0:40,0:40:99:0,103,1210	0/0:36,0:36:99:0,103,1055	0/0:39,0:39:99:0,104,1179	0/0:17,0:17:51:0,51,471	0/0:39,0:39:99:0,110,1170	0/0:35,0:35:99:0,105,1040	0/0:36,0:36:99:0,99,1030	0/0:32,0:32:0:0,0,266	0/0:43,0:43:99:0,100,1295	0/0:35,0:35:99:0,105,1071	0/0:34,0:34:99:0,99,1056	0/0:34,0:34:99:0,102,1031	./.:36,0:36:.:0,0,0	0/1:28,21:49:99:493,0,646	0/0:42,0:42:99:0,101,1499	0/0:41,0:41:99:0,103,1368
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf
index 6d4b19d1716..2ab46c8f422 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf
@@ -9,7 +9,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.nocall.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:15 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -116,7 +115,6 @@
 ##contig=<ID=GL000192.1,length=547496>
 ##contig=<ID=NC_007605,length=171823>
 ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
-##source=GenotypeGVCFs
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample_0	Sample_1	Sample_10	Sample_100	Sample_101	Sample_102	Sample_103	Sample_104	Sample_105	Sample_106	Sample_107	Sample_108	Sample_109	Sample_11	Sample_110	Sample_111	Sample_112	Sample_113	Sample_114	Sample_115	Sample_116	Sample_117	Sample_118	Sample_119	Sample_12	Sample_120	Sample_121	Sample_122	Sample_123	Sample_124	Sample_125	Sample_126	Sample_127	Sample_128	Sample_129	Sample_13	Sample_130	Sample_131	Sample_132	Sample_133	Sample_134	Sample_135	Sample_136	Sample_137	Sample_138	Sample_139	Sample_14	Sample_140	Sample_141	Sample_142	Sample_143	Sample_144	Sample_145	Sample_146	Sample_147	Sample_148	Sample_149	Sample_15	Sample_150	Sample_151	Sample_152	Sample_153	Sample_154	Sample_155	Sample_156	Sample_157	Sample_158	Sample_159	Sample_16	Sample_160	Sample_161	Sample_162	Sample_163	Sample_164	Sample_165	Sample_166	Sample_167	Sample_168	Sample_169	Sample_17	Sample_170	Sample_171	Sample_172	Sample_173	Sample_174	Sample_175	Sample_176	Sample_177	Sample_178	Sample_179	Sample_18	Sample_180	Sample_181	Sample_182	Sample_183	Sample_184	Sample_185	Sample_186	Sample_187	Sample_188	Sample_189	Sample_19	Sample_190	Sample_191	Sample_192	Sample_193	Sample_194	Sample_195	Sample_196	Sample_197	Sample_198	Sample_199	Sample_2	Sample_20	Sample_200	Sample_201	Sample_202	Sample_203	Sample_204	Sample_205	Sample_206	Sample_207	Sample_208	Sample_209	Sample_21	Sample_210	Sample_211	Sample_212	Sample_213	Sample_214	Sample_215	Sample_216	Sample_217	Sample_218	Sample_219	Sample_22	Sample_220	Sample_221	Sample_222	Sample_223	Sample_224	Sample_225	Sample_226	Sample_227	Sample_228	Sample_229	Sample_23	Sample_230	Sample_231	Sample_232	Sample_233	Sample_234	Sample_235	Sample_236	Sample_237	Sample_238	Sample_239	Sample_24	Sample_240	Sample_241	Sample_242	Sample_243	Sample_244	Sample_245	Sample_246	Sample_247	Sample_248	Sample_249	Sample_25	Sample_250	Sample_251	Sample_252	Sample_253	Sample_254	Sample_255	Sample_256	Sample_257	Sample_258	Sample_259	Sample_26	Sample_260	Sample_261	Sample_262	Sample_263	Sample_264	Sample_265	Sample_266	Sample_267	Sample_268	Sample_269	Sample_27	Sample_270	Sample_271	Sample_272	Sample_273	Sample_274	Sample_275	Sample_276	Sample_277	Sample_278	Sample_279	Sample_28	Sample_280	Sample_281	Sample_282	Sample_283	Sample_284	Sample_285	Sample_286	Sample_287	Sample_288	Sample_289	Sample_29	Sample_290	Sample_291	Sample_292	Sample_293	Sample_294	Sample_295	Sample_296	Sample_297	Sample_298	Sample_3	Sample_30	Sample_31	Sample_32	Sample_33	Sample_34	Sample_35	Sample_36	Sample_37	Sample_38	Sample_39	Sample_4	Sample_40	Sample_41	Sample_42	Sample_43	Sample_44	Sample_45	Sample_46	Sample_47	Sample_48	Sample_49	Sample_5	Sample_50	Sample_51	Sample_52	Sample_53	Sample_54	Sample_55	Sample_56	Sample_57	Sample_58	Sample_59	Sample_6	Sample_60	Sample_61	Sample_62	Sample_63	Sample_64	Sample_65	Sample_66	Sample_67	Sample_68	Sample_69	Sample_7	Sample_70	Sample_71	Sample_72	Sample_73	Sample_74	Sample_75	Sample_76	Sample_77	Sample_78	Sample_79	Sample_8	Sample_80	Sample_81	Sample_82	Sample_83	Sample_84	Sample_85	Sample_86	Sample_87	Sample_88	Sample_89	Sample_9	Sample_90	Sample_91	Sample_92	Sample_93	Sample_94	Sample_95	Sample_96	Sample_97	Sample_98	Sample_99
-20	1115540	.	AC	A	557.01	.	AC=3;AF=5.017e-03;AN=598;BaseQRankSum=-3.770e-01;DP=3640;ExcessHet=3.0541;FS=0.000;InbreedingCoeff=-0.0217;MLEAC=3;MLEAF=5.017e-03;MQ=59.68;MQ0=0;MQRankSum=1.00;QD=12.38;ReadPosRankSum=0.462;SOR=0.760	GT:AD:DP:GQ:PL	0/0:12,0:12:36:0,36,406	0/0:12,0:12:31:0,31,464	0/0:8,0:8:18:0,18,270	0/0:10,0:10:21:0,21,315	0/0:5,0:5:15:0,15,211	0/0:7,0:7:21:0,21,242	0/0:22,0:22:60:0,60,678	0/0:12,0:12:28:0,28,423	0/0:7,0:7:21:0,21,213	0/0:9,0:9:21:0,21,315	0/0:10,0:10:30:0,30,335	0/0:8,0:8:21:0,21,315	0/0:24,0:24:60:0,60,823	0/0:6,0:6:12:0,12,164	0/0:12,0:12:27:0,27,396	0/0:2,0:2:6:0,6,64	0/0:9,0:9:21:0,21,308	0/0:21,0:21:60:0,60,900	0/0:23,0:23:60:0,60,750	0/0:9,0:9:21:0,21,312	0/0:5,0:5:9:0,9,135	0/0:12,0:12:24:0,24,360	0/0:7,0:7:21:0,21,249	0/0:10,0:10:21:0,21,312	0/0:10,0:10:21:0,21,315	0/0:10,0:10:21:0,21,315	0/0:7,0:7:21:0,21,222	0/0:9,0:9:14:0,14,212	0/0:14,0:14:36:0,36,464	0/0:25,0:25:69:0,69,1035	0/0:9,0:9:21:0,21,315	0/0:9,0:9:24:0,24,360	0/0:5,0:5:12:0,12,158	0/0:21,0:21:60:0,60,900	0/0:11,0:11:21:0,21,315	0/0:9,0:9:21:0,21,281	0/0:10,0:10:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:8,0:8:20:0,20,254	0/0:11,0:11:21:0,21,315	0/0:5,0:5:12:0,12,180	0/0:7,0:7:21:0,21,260	0/0:2,0:2:6:0,6,70	0/0:23,0:23:60:0,60,807	0/0:4,0:4:6:0,6,90	0/0:10,0:10:27:0,27,323	0/0:7,0:7:21:0,21,220	0/0:11,0:11:21:0,21,315	0/0:13,0:13:26:0,26,417	0/0:6,0:6:9:0,9,135	0/0:6,0:6:18:0,18,185	0/0:6,0:6:0:0,0,96	0/0:7,0:7:21:0,21,252	0/0:9,0:9:21:0,21,315	0/0:2,0:2:6:0,6,68	0/0:9,0:9:24:0,24,309	0/0:3,0:3:6:0,6,90	0/0:11,0:11:24:0,24,347	0/0:8,0:8:21:0,21,264	0/0:8,0:8:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:31,0:31:81:0,81,1215	0/0:24,0:24:60:0,60,900	0/0:17,0:17:26:0,26,578	0/0:13,0:13:19:0,19,401	0/0:9,0:9:24:0,24,295	0/0:22,0:22:60:0,60,770	0/0:24,0:24:63:0,63,945	0/0:8,0:8:21:0,21,315	0/0:7,0:7:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:6,0:6:18:0,18,201	0/0:5,0:5:15:0,15,154	0/0:24,0:24:60:0,60,900	0/0:25,0:25:60:0,60,900	0/0:7,0:7:21:0,21,281	0/0:2,0:2:6:0,6,74	0/0:19,0:19:42:0,42,630	0/0:22,0:22:60:0,60,890	0/0:9,0:9:21:0,21,315	0/0:25,0:25:60:0,60,882	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,96	0/0:7,0:7:21:0,21,242	0/0:7,0:7:21:0,21,293	0/0:9,0:9:27:0,27,294	0/0:3,0:3:9:0,9,98	0/0:9,0:9:21:0,21,315	0/0:6,0:6:18:0,18,182	0/0:8,0:8:12:0,12,216	0/0:9,0:9:21:0,21,315	0/0:6,0:6:12:0,12,180	0/0:7,0:7:18:0,18,270	0/0:7,0:7:21:0,21,222	0/0:4,0:4:6:0,6,90	0/0:7,0:7:21:0,21,245	0/0:6,0:6:15:0,15,178	0/0:4,0:4:6:0,6,90	0/0:9,0:9:21:0,21,276	0/0:8,0:8:21:0,21,315	0/0:5,0:5:9:0,9,135	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,90	0/0:3,0:3:9:0,9,109	0/0:7,0:7:21:0,21,240	0/0:5,0:5:12:0,12,180	0/0:29,0:29:75:0,75,1125	0/0:8,0:8:21:0,21,315	0/0:14,0:14:30:0,30,450	0/0:10,0:10:24:0,24,360	0/0:7,0:7:21:0,21,210	0/0:16,0:16:39:0,39,540	0/0:12,0:12:23:0,23,401	0/0:5,0:5:9:0,9,135	0/0:20,0:20:52:0,52,695	0/0:25,0:25:60:0,60,900	0/0:9,0:9:21:0,21,284	0/0:9,0:9:24:0,24,360	0/0:18,0:18:51:0,51,596	0/0:14,0:14:27:0,27,405	0/0:15,0:15:39:0,39,579	0/0:22,0:22:60:0,60,729	0/0:8,0:8:21:0,21,308	0/0:13,0:13:26:0,26,450	0/0:19,0:19:36:0,36,628	0/1:12,11:23:99:291,0,321	0/0:15,0:15:24:0,24,450	0/0:10,0:10:21:0,21,315	0/0:11,0:11:33:0,33,408	0/0:21,0:21:51:0,51,765	0/0:15,0:15:20:0,20,540	0/0:12,0:12:27:0,27,405	0/0:9,0:9:21:0,21,315	0/0:12,0:12:27:0,27,405	0/0:22,0:22:60:0,60,900	0/0:8,0:8:21:0,21,295	0/0:2,0:2:6:0,6,64	0/0:14,0:14:28:0,28,437	0/0:2,0:2:6:0,6,76	0/0:27,0:27:60:0,60,900	0/0:9,0:9:13:0,13,243	0/0:6,0:6:12:0,12,180	0/0:9,0:9:21:0,21,296	0/0:11,0:11:30:0,30,343	0/0:6,0:6:18:0,18,216	0/0:24,0:24:61:0,61,945	0/0:14,0:14:27:0,27,405	0/0:5,0:5:9:0,9,135	0/0:5,0:5:9:0,9,135	0/0:10,0:10:21:0,21,360	0/0:7,0:7:21:0,21,235	0/0:2,0:2:6:0,6,65	0/0:3,0:3:6:0,6,90	0/0:25,0:25:60:0,60,900	0/0:14,0:14:22:0,22,532	0/0:4,0:4:6:0,6,90	0/0:8,0:8:21:0,21,273	0/0:24,0:24:63:0,63,945	0/0:2,0:2:6:0,6,67	0/0:18,0:18:33:0,33,495	0/0:8,0:8:21:0,21,238	0/0:11,0:11:24:0,24,320	0/0:23,0:23:60:0,60,900	0/0:23,0:23:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:10,0:10:24:0,24,360	0/0:22,0:22:60:0,60,772	0/0:8,0:8:20:0,20,315	0/0:22,0:22:60:0,60,900	0/0:21,0:21:60:0,60,657	0/0:13,0:13:22:0,22,450	0/0:7,0:7:21:0,21,253	0/0:9,0:9:20:0,20,322	0/0:4,0:4:12:0,12,147	0/0:9,0:9:27:0,27,302	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,281	0/0:7,0:7:21:0,21,261	0/0:10,0:10:24:0,24,360	0/0:10,0:10:24:0,24,360	0/0:8,0:8:21:0,21,315	0/0:9,0:9:24:0,24,318	0/0:24,0:24:60:0,60,900	0/0:26,0:26:63:0,63,945	0/0:8,0:8:21:0,21,283	0/1:3,6:9:70:169,0,70	0/0:8,0:8:21:0,21,315	0/0:2,0:2:6:0,6,62	0/0:8,0:8:21:0,21,247	0/0:3,0:3:6:0,6,87	0/0:23,0:23:60:0,60,900	0/0:2,0:2:6:0,6,67	0/0:5,0:5:6:0,6,90	0/0:3,0:3:6:0,6,90	0/0:8,0:8:21:0,21,285	0/0:8,0:8:18:0,18,270	0/0:5,0:5:9:0,9,135	0/0:9,0:9:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:8,0:8:24:0,24,258	0/0:9,0:9:24:0,24,360	0/0:5,0:5:3:0,3,125	0/0:8,0:8:21:0,21,231	0/0:6,0:6:15:0,15,225	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,219	0/0:5,0:5:12:0,12,158	0/0:4,0:4:9:0,9,130	0/0:7,0:7:21:0,21,237	0/0:26,0:26:60:0,60,895	0/0:24,0:24:60:0,60,850	0/0:7,0:7:21:0,21,272	0/0:8,0:8:22:0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+20	1115540	.	AC	A	557.01	.	AC=3;AF=5.017e-03;AN=598;BaseQRankSum=-3.770e-01;DP=3640;ExcessHet=3.0323;FS=0.000;InbreedingCoeff=-0.0217;MLEAC=3;MLEAF=5.017e-03;MQ=59.68;MQ0=0;MQRankSum=1.00;QD=12.38;ReadPosRankSum=0.462;SOR=0.760	GT:AD:DP:GQ:PL	0/0:12,0:12:36:0,36,406	0/0:12,0:12:31:0,31,464	0/0:8,0:8:18:0,18,270	0/0:10,0:10:21:0,21,315	0/0:5,0:5:15:0,15,211	0/0:7,0:7:21:0,21,242	0/0:22,0:22:60:0,60,678	0/0:12,0:12:28:0,28,423	0/0:7,0:7:21:0,21,213	0/0:9,0:9:21:0,21,315	0/0:10,0:10:30:0,30,335	0/0:8,0:8:21:0,21,315	0/0:24,0:24:60:0,60,823	0/0:6,0:6:12:0,12,164	0/0:12,0:12:27:0,27,396	0/0:2,0:2:6:0,6,64	0/0:9,0:9:21:0,21,308	0/0:21,0:21:60:0,60,900	0/0:23,0:23:60:0,60,750	0/0:9,0:9:21:0,21,312	0/0:5,0:5:9:0,9,135	0/0:12,0:12:24:0,24,360	0/0:7,0:7:21:0,21,249	0/0:10,0:10:21:0,21,312	0/0:10,0:10:21:0,21,315	0/0:10,0:10:21:0,21,315	0/0:7,0:7:21:0,21,222	0/0:9,0:9:14:0,14,212	0/0:14,0:14:36:0,36,464	0/0:25,0:25:69:0,69,1035	0/0:9,0:9:21:0,21,315	0/0:9,0:9:24:0,24,360	0/0:5,0:5:12:0,12,158	0/0:21,0:21:60:0,60,900	0/0:11,0:11:21:0,21,315	0/0:9,0:9:21:0,21,281	0/0:10,0:10:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:8,0:8:20:0,20,254	0/0:11,0:11:21:0,21,315	0/0:5,0:5:12:0,12,180	0/0:7,0:7:21:0,21,260	0/0:2,0:2:6:0,6,70	0/0:23,0:23:60:0,60,807	0/0:4,0:4:6:0,6,90	0/0:10,0:10:27:0,27,323	0/0:7,0:7:21:0,21,220	0/0:11,0:11:21:0,21,315	0/0:13,0:13:26:0,26,417	0/0:6,0:6:9:0,9,135	0/0:6,0:6:18:0,18,185	0/0:6,0:6:0:0,0,96	0/0:7,0:7:21:0,21,252	0/0:9,0:9:21:0,21,315	0/0:2,0:2:6:0,6,68	0/0:9,0:9:24:0,24,309	0/0:3,0:3:6:0,6,90	0/0:11,0:11:24:0,24,347	0/0:8,0:8:21:0,21,264	0/0:8,0:8:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:31,0:31:81:0,81,1215	0/0:24,0:24:60:0,60,900	0/0:17,0:17:26:0,26,578	0/0:13,0:13:19:0,19,401	0/0:9,0:9:24:0,24,295	0/0:22,0:22:60:0,60,770	0/0:24,0:24:63:0,63,945	0/0:8,0:8:21:0,21,315	0/0:7,0:7:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:6,0:6:18:0,18,201	0/0:5,0:5:15:0,15,154	0/0:24,0:24:60:0,60,900	0/0:25,0:25:60:0,60,900	0/0:7,0:7:21:0,21,281	0/0:2,0:2:6:0,6,74	0/0:19,0:19:42:0,42,630	0/0:22,0:22:60:0,60,890	0/0:9,0:9:21:0,21,315	0/0:25,0:25:60:0,60,882	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,96	0/0:7,0:7:21:0,21,242	0/0:7,0:7:21:0,21,293	0/0:9,0:9:27:0,27,294	0/0:3,0:3:9:0,9,98	0/0:9,0:9:21:0,21,315	0/0:6,0:6:18:0,18,182	0/0:8,0:8:12:0,12,216	0/0:9,0:9:21:0,21,315	0/0:6,0:6:12:0,12,180	0/0:7,0:7:18:0,18,270	0/0:7,0:7:21:0,21,222	0/0:4,0:4:6:0,6,90	0/0:7,0:7:21:0,21,245	0/0:6,0:6:15:0,15,178	0/0:4,0:4:6:0,6,90	0/0:9,0:9:21:0,21,276	0/0:8,0:8:21:0,21,315	0/0:5,0:5:9:0,9,135	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,90	0/0:3,0:3:9:0,9,109	0/0:7,0:7:21:0,21,240	0/0:5,0:5:12:0,12,180	0/0:29,0:29:75:0,75,1125	0/0:8,0:8:21:0,21,315	0/0:14,0:14:30:0,30,450	0/0:10,0:10:24:0,24,360	0/0:7,0:7:21:0,21,210	0/0:16,0:16:39:0,39,540	0/0:12,0:12:23:0,23,401	0/0:5,0:5:9:0,9,135	0/0:20,0:20:52:0,52,695	0/0:25,0:25:60:0,60,900	0/0:9,0:9:21:0,21,284	0/0:9,0:9:24:0,24,360	0/0:18,0:18:51:0,51,596	0/0:14,0:14:27:0,27,405	0/0:15,0:15:39:0,39,579	0/0:22,0:22:60:0,60,729	0/0:8,0:8:21:0,21,308	0/0:13,0:13:26:0,26,450	0/0:19,0:19:36:0,36,628	0/1:12,11:23:99:291,0,321	0/0:15,0:15:24:0,24,450	0/0:10,0:10:21:0,21,315	0/0:11,0:11:33:0,33,408	0/0:21,0:21:51:0,51,765	0/0:15,0:15:20:0,20,540	0/0:12,0:12:27:0,27,405	0/0:9,0:9:21:0,21,315	0/0:12,0:12:27:0,27,405	0/0:22,0:22:60:0,60,900	0/0:8,0:8:21:0,21,295	0/0:2,0:2:6:0,6,64	0/0:14,0:14:28:0,28,437	0/0:2,0:2:6:0,6,76	0/0:27,0:27:60:0,60,900	0/0:9,0:9:13:0,13,243	0/0:6,0:6:12:0,12,180	0/0:9,0:9:21:0,21,296	0/0:11,0:11:30:0,30,343	0/0:6,0:6:18:0,18,216	0/0:24,0:24:61:0,61,945	0/0:14,0:14:27:0,27,405	0/0:5,0:5:9:0,9,135	0/0:5,0:5:9:0,9,135	0/0:10,0:10:21:0,21,360	0/0:7,0:7:21:0,21,235	0/0:2,0:2:6:0,6,65	0/0:3,0:3:6:0,6,90	0/0:25,0:25:60:0,60,900	0/0:14,0:14:22:0,22,532	0/0:4,0:4:6:0,6,90	0/0:8,0:8:21:0,21,273	0/0:24,0:24:63:0,63,945	0/0:2,0:2:6:0,6,67	0/0:18,0:18:33:0,33,495	0/0:8,0:8:21:0,21,238	0/0:11,0:11:24:0,24,320	0/0:23,0:23:60:0,60,900	0/0:23,0:23:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:10,0:10:24:0,24,360	0/0:22,0:22:60:0,60,772	0/0:8,0:8:20:0,20,315	0/0:22,0:22:60:0,60,900	0/0:21,0:21:60:0,60,657	0/0:13,0:13:22:0,22,450	0/0:7,0:7:21:0,21,253	0/0:9,0:9:20:0,20,322	0/0:4,0:4:12:0,12,147	0/0:9,0:9:27:0,27,302	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,281	0/0:7,0:7:21:0,21,261	0/0:10,0:10:24:0,24,360	0/0:10,0:10:24:0,24,360	0/0:8,0:8:21:0,21,315	0/0:9,0:9:24:0,24,318	0/0:24,0:24:60:0,60,900	0/0:26,0:26:63:0,63,945	0/0:8,0:8:21:0,21,283	0/1:3,6:9:70:169,0,70	0/0:8,0:8:21:0,21,315	0/0:2,0:2:6:0,6,62	0/0:8,0:8:21:0,21,247	0/0:3,0:3:6:0,6,87	0/0:23,0:23:60:0,60,900	0/0:2,0:2:6:0,6,67	0/0:5,0:5:6:0,6,90	0/0:3,0:3:6:0,6,90	0/0:8,0:8:21:0,21,285	0/0:8,0:8:18:0,18,270	0/0:5,0:5:9:0,9,135	0/0:9,0:9:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:8,0:8:24:0,24,258	0/0:9,0:9:24:0,24,360	0/0:5,0:5:3:0,3,125	0/0:8,0:8:21:0,21,231	0/0:6,0:6:15:0,15,225	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,219	0/0:5,0:5:12:0,12,158	0/0:4,0:4:9:0,9,130	0/0:7,0:7:21:0,21,237	0/0:26,0:26:60:0,60,895	0/0:24,0:24:60:0,60,850	0/0:7,0:7:21:0,21,272	0/0:8,0:8:22:0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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected.posteriors.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected.posteriors.genotyped.vcf
index 22c1373503f..c6ebe09830c 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected.posteriors.genotyped.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected.posteriors.genotyped.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=PP,Number=G,Type=Integer,Description="Phred-scaled Posterior Genotype Probabilities">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected.posteriors.genotyped.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/../../GenomicsDBImport/expected.testGVCFMode.gatk4.posteriors.g.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:18:42 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -35,257 +34,256 @@
 ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
 ##contig=<ID=20,length=63025520>
 ##contig=<ID=21,length=48129895>
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	.	C	T	926.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.913;QD=14.48;RAW_MQ=228169.00;ReadPosRankSum=-1.790e-01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
-20	10000211	.	C	T	962.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.06;QD=18.16;RAW_MQ=192169.00;ReadPosRankSum=1.07;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
-20	10000439	.	T	G	2819.03	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=25.36;RAW_MQ=279076.00;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0
-20	10000598	.	T	A	1956.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=28.73;RAW_MQ=149628.00;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0
-20	10000694	.	G	A	1029.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.60;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.66;MQRankSum=-5.114e+00;QD=12.56;RAW_MQ=194196.00;ReadPosRankSum=0.182;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601
-20	10000758	.	T	A	3853.03	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=30.97;RAW_MQ=270581.00;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0
-20	10001019	.	T	G	671.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.541e+00;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=49.49;MQRankSum=-7.498e+00;QD=10.33;RAW_MQ=159195.00;ReadPosRankSum=-1.497e+00;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426
-20	10001298	.	T	A	2932.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=27.24;RAW_MQ=218493.00;SOR=0.963	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0
-20	10001436	.	A	AAGGCT	2325.06	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.88;QD=28.20;RAW_MQ=93596.00;SOR=3.442	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2339,156,0
-20	10001474	.	C	T	2655.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;QD=25.00;RAW_MQ=141456.00;SOR=1.516	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0
-20	10001617	.	C	A	1752.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.26;ClippingRankSum=0.00;DP=103;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=1.37;QD=17.02;RAW_MQ=358589.00;ReadPosRankSum=-5.780e-01;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781
-20	10001628	.	G	A	3913.03	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=29.56;RAW_MQ=332548.00;SOR=1.053	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0
-20	10001661	.	T	C	3621.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=30.62;RAW_MQ=275574.00;SOR=1.193	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0
-20	10001670	.	T	G	3688.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=28.17;RAW_MQ=267297.00;SOR=0.995	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0
-20	10002058	.	T	G	2978.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.00;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;MQRankSum=3.07;QD=26.80;RAW_MQ=250206.00;ReadPosRankSum=-5.240e-01;SOR=0.776	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0
-20	10002099	.	C	T	1215.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820e-01;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-8.500e-01;QD=18.70;RAW_MQ=209529.00;ReadPosRankSum=-3.600e-01;SOR=0.375	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844
-20	10002138	.	C	G	2458.03	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.38;QD=26.00;RAW_MQ=168463.00;SOR=0.730	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0
-20	10002142	.	G	C	2422.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.31;QD=30.02;RAW_MQ=164863.00;SOR=0.853	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,52:52:99:1|1:10002138_C_G:2436,166,0
-20	10002458	.	G	GTTT	2155.04	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.07;QD=31.98;RAW_MQ=127415.00;SOR=2.049	GT:AD:DP:GQ:PL	1/1:0,6:16:99:2090,167,0
-20	10002470	.	C	T	2537.03	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;QD=27.51;RAW_MQ=144226.00;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2551,189,0
-20	10002625	.	G	T	2680.03	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=29.11;RAW_MQ=223179.00;SOR=1.127	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0
-20	10003021	.	C	T	2398.03	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;QD=28.08;RAW_MQ=208779.00;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0
-20	10003358	.	A	C	1475.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.000e-03;ClippingRankSum=0.00;DP=90;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.01;QD=16.58;RAW_MQ=321769.00;ReadPosRankSum=-4.440e-01;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477
-20	10003651	.	T	C	3635.03	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=23.23;RAW_MQ=325876.00;SOR=1.511	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0
-20	10003692	.	A	G	2624.03	.	AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=29.03;RAW_MQ=240338.00;SOR=1.352	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0
-20	10003832	.	G	A	2720.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;QD=30.67;RAW_MQ=215436.00;SOR=1.473	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0
-20	10004094	.	A	C	1840.03	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;QD=34.72;RAW_MQ=147492.00;SOR=1.524	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0
-20	10004147	.	A	G	1852.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;QD=26.61;RAW_MQ=157262.00;SOR=1.136	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0
-20	10004193	.	G	T	939.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.040e-01;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=2.391;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=3.42;QD=18.07;RAW_MQ=186469.00;ReadPosRankSum=0.775;SOR=1.019	GT:AD:DP:GQ:PL	0/1:23,29:52:99:947,0,775
-20	10004222	.	C	CA	42.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;ClippingRankSum=0.00;DP=55;ExcessHet=3.0103;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.05;MQRankSum=-2.042e+00;QD=1.09;RAW_MQ=198329.00;ReadPosRankSum=-5.200e-02;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,8:39:50:50,0,923
-20	10004223	.	A	AG	77.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.320e-01;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQRankSum=1.89;QD=1.65;RAW_MQ=214369.00;ReadPosRankSum=2.23;SOR=0.638	GT:AD:DP:GQ:PL	0/1:36,11:47:85:85,0,982
-20	10004351	.	C	G	2770.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=29.20;RAW_MQ=243987.00;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2784,211,0
-20	10004389	.	T	G	2509.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;QD=28.55;RAW_MQ=199570.00;SOR=1.143	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0
-20	10004610	.	A	C	3640.03	.	AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;QD=34.42;RAW_MQ=306605.00;SOR=0.761	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0
-20	10004725	.	A	G	972.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.154e+00;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.27;MQRankSum=3.01;QD=14.96;RAW_MQ=198562.00;ReadPosRankSum=1.79;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168
-20	10004769	.	TAAAACTATGC	T	1011.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.60;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.37;MQRankSum=-6.625e+00;QD=15.81;RAW_MQ=216626.00;ReadPosRankSum=2.22;SOR=1.306	GT:AD:DP:GQ:PL	0/1:37,27:64:99:1019,0,1471
-20	10004874	.	A	C	3617.03	.	AC=2;AF=1.00;AN=2;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=28.53;RAW_MQ=306223.00;SOR=1.286	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0
-20	10004887	.	A	G	1344.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.20;MQRankSum=-6.700e-02;QD=15.82;RAW_MQ=304923.00;ReadPosRankSum=-1.600e-01;SOR=0.984	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,40:85:99:0|1:10004874_A_C:1352,0,1542
-20	10005010	.	C	T	2949.03	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=27.23;RAW_MQ=256441.00;SOR=1.226	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2963,217,0
-20	10005427	.	C	T	2229.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;QD=29.52;RAW_MQ=195241.00;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2243,165,0
-20	10005499	.	A	G	3068.03	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.47;RAW_MQ=273600.00;SOR=1.121	GT:AD:DP:GQ:PL	1/1:0,76:76:99:3082,229,0
-20	10005587	.	A	G	1250.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.340e-01;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-9.720e-01;QD=17.37;RAW_MQ=257810.00;ReadPosRankSum=0.649;SOR=0.848	GT:AD:DP:GQ:PL	0/1:36,36:72:99:1258,0,1236
-20	10005723	.	A	G	3077.03	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=32.91;RAW_MQ=307369.00;SOR=0.947	GT:AD:DP:GQ:PL	1/1:0,86:86:99:3091,258,0
-20	10006291	.	G	A	999.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;ClippingRankSum=0.00;DP=84;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.500;MQ=59.28;MQRankSum=-1.081e+00;QD=11.90;RAW_MQ=295179.00;ReadPosRankSum=-1.614e+00;SOR=0.659	GT:AD:DP:GQ:PL	0/1:53,31:84:99:1007,0,1905
-20	10006404	.	A	C	2943.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.16;QD=31.31;RAW_MQ=269451.00;SOR=1.432	GT:AD:DP:GQ:PL	1/1:0,76:76:99:2957,228,0
-20	10006682	.	T	A	2889.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=31.45;RAW_MQ=257810.00;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2903,219,0
-20	10006819	.	AAAAC	A	2555.03	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.13;QD=33.27;RAW_MQ=284000.00;SOR=0.762	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2569,176,0
-20	10007150	.	G	C	690.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.476e+00;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.96;RAW_MQ=226800.00;ReadPosRankSum=-1.745e+00;SOR=0.746	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479
-20	10007175	.	C	T	1371.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;ClippingRankSum=0.00;DP=61;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=1.32;QD=22.49;RAW_MQ=216841.00;ReadPosRankSum=-7.300e-01;SOR=0.434	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780
-20	10007352	.	C	T	2779.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=31.26;RAW_MQ=249241.00;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0
-20	10007531	.	A	G	2935.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;QD=27.76;RAW_MQ=260569.00;SOR=1.577	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2949,217,0
-20	10007980	.	A	C	3539.03	.	AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;QD=29.09;RAW_MQ=331800.00;SOR=0.990	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0
-20	10008029	.	T	TA	2010.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;ClippingRankSum=0.00;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.98;MQRankSum=0.576;QD=26.80;RAW_MQ=327251.00;ReadPosRankSum=-1.055e+00;SOR=0.788	GT:AD:DP:GQ:PL	1/1:3,72:75:99:2024,145,0
-20	10008146	.	TA	T	2165.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.59;QD=30.93;RAW_MQ=268000.00;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2179,211,0
-20	10008221	.	T	C	3239.03	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=26.08;RAW_MQ=289669.00;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0
-20	10008458	.	T	G	2669.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.54;QD=33.85;RAW_MQ=193211.00;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0
-20	10008742	.	G	T	736.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.89;ClippingRankSum=0.00;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.502e+00;QD=15.03;RAW_MQ=67874.00;ReadPosRankSum=0.772;SOR=0.741	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580
-20	10008758	.	C	CA	707.53	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;ClippingRankSum=0.00;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-1.168e+00;QD=20.22;RAW_MQ=54656.00;ReadPosRankSum=-2.340e-01;SOR=0.249	GT:AD:DP:GQ:PL	1/1:4,31:35:10:721,10,0
-20	10008921	.	C	CA	283.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;ClippingRankSum=0.00;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.906e+00;QD=8.34;RAW_MQ=155512.00;ReadPosRankSum=-4.150e-01;SOR=0.512	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:34:99:0|1:10008921_C_CA:291,0,366
-20	10008948	.	TA	T	2081.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.30;MQRankSum=2.05;QD=27.08;RAW_MQ=139463.00;ReadPosRankSum=0.749;SOR=0.818	GT:AD:DP:GQ:PGT:PID:PL	1/1:1,50:51:99:1|1:10008921_C_CA:2095,107,0
-20	10008952	.	CACACACACACA	C,CCACACACACA	1687.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.941;ClippingRankSum=0.00;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.81;MQRankSum=1.84;QD=25.42;RAW_MQ=154909.00;ReadPosRankSum=0.685;SOR=1.127	GT:AD:DP:GQ:PL	1/2:1,14,11:34:99:1704,525,845,582,0,530
-20	10009227	.	A	G	1390.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220e+00;ClippingRankSum=0.00;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.43;QD=22.43;RAW_MQ=202588.00;ReadPosRankSum=-1.093e+00;SOR=0.281	GT:AD:DP:GQ:PL	0/1:23,39:62:99:1398,0,740
-20	10009246	.	A	G	3017.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=27.65;RAW_MQ=242208.00;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3031,231,0
-20	10009400	.	T	A	3013.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;RAW_MQ=266400.00;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0
-20	10009512	.	C	G	3054.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.47;QD=30.56;RAW_MQ=263240.00;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3068,231,0
-20	10009719	.	A	G	1910.03	.	AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.29;QD=32.37;RAW_MQ=207410.00;SOR=0.950	GT:AD:DP:GQ:PL	1/1:0,59:59:99:1924,175,0
-20	10009795	.	A	G	1895.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=33.63;RAW_MQ=166969.00;SOR=1.514	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1909,141,0
-20	10009842	.	G	GAA	562.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.872;ClippingRankSum=0.00;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQRankSum=-6.030e-01;QD=16.55;RAW_MQ=150092.00;ReadPosRankSum=0.052;SOR=0.738	GT:AD:DP:GQ:PL	0/1:19,15:34:99:570,0,690
-20	10009844	.	G	A	682.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.05;ClippingRankSum=0.00;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.72;MQRankSum=0.975;QD=19.50;RAW_MQ=147168.00;ReadPosRankSum=0.259;SOR=0.793	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,19:35:99:0|1:10009844_G_A:690,0,586
-20	10009871	.	A	G	679.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.030e-01;ClippingRankSum=0.00;DP=61;ExcessHet=3.0103;FS=2.798;MLEAC=1;MLEAF=0.500;MQ=50.95;MQRankSum=1.50;QD=18.88;RAW_MQ=158337.00;ReadPosRankSum=1.57;SOR=0.553	GT:AD:DP:GQ:PGT:PID:PL	0/1:17,19:36:99:0|1:10009844_G_A:687,0,594
-20	10009875	.	A	G,AGGGAGG	2390.06	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.378;ClippingRankSum=0.00;DP=58;ExcessHet=3.0103;FS=6.794;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.44;MQRankSum=1.36;QD=30.55;RAW_MQ=147537.00;ReadPosRankSum=-8.300e-02;SOR=0.599	GT:AD:DP:GQ:PL	1/2:2,15,13:30:99:2407,645,533,697,0,574
-20	10009879	.	A	G	2259.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.53;ClippingRankSum=0.00;DP=50;ExcessHet=3.0103;FS=9.369;MLEAC=2;MLEAF=1.00;MQ=49.85;MQRankSum=1.57;QD=32.62;RAW_MQ=124261.00;ReadPosRankSum=1.39;SOR=1.474	GT:AD:DP:GQ:PL	1/1:2,47:49:99:2273,150,0
-20	10009883	.	A	G	2166.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.56;QD=29.33;RAW_MQ=132938.00;SOR=1.659	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2180,147,0
-20	10010393	.	T	G	1485.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.351e+00;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.284e+00;QD=18.81;RAW_MQ=278882.00;ReadPosRankSum=-1.630e+00;SOR=0.606	GT:AD:DP:GQ:PL	0/1:36,43:79:99:1493,0,1230
-20	10010536	.	G	GA	2486.06	.	AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.63;QD=31.47;RAW_MQ=322900.00;SOR=0.881	GT:AD:DP:GQ:PL	1/1:0,79:79:99:2500,243,0
-20	10010766	.	T	G	2426.03	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.36;RAW_MQ=241200.00;SOR=0.818	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2440,199,0
-20	10010832	.	T	C	2966.03	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;QD=34.30;RAW_MQ=265538.00;SOR=1.091	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2980,226,0
-20	10011075	.	C	T	1346.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.36;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.22;RAW_MQ=306000.00;ReadPosRankSum=-1.057e+00;SOR=0.968	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1354,0,1333
-20	10011309	.	T	C	2707.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.00;RAW_MQ=277200.00;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2721,231,0
-20	10011517	.	GA	G	520.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.690;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=3.171;MLEAC=1;MLEAF=0.500;MQ=59.90;MQRankSum=1.80;QD=8.01;RAW_MQ=326510.00;ReadPosRankSum=1.15;SOR=0.394	GT:AD:DP:GQ:PL	0/1:37,28:73:99:528,0,875
-20	10011666	.	C	T	2976.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=30.82;RAW_MQ=254523.00;SOR=1.103	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2990,220,0
-20	10011939	.	C	T	2484.03	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.26;QD=29.27;RAW_MQ=193043.00;SOR=1.292	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2498,184,0
-20	10012021	.	CA	C	1999.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;QD=30.29;RAW_MQ=228076.00;SOR=1.196	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2013,198,0
-20	10012362	.	G	T	850.03	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.78;QD=35.92;RAW_MQ=66527.00;SOR=4.003	GT:AD:DP:GQ:PL	1/1:0,23:23:69:864,69,0
-20	10012384	.	T	C	250.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.773e+00;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.500;MQ=53.75;MQRankSum=-8.110e-01;QD=13.92;RAW_MQ=54886.00;ReadPosRankSum=0.190;SOR=0.044	GT:AD:DP:GQ:PL	0/1:10,8:18:99:258,0,355
-20	10012387	.	T	C	548.03	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.96;QD=34.25;RAW_MQ=47686.00;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,16:16:50:562,50,0
-20	10012479	.	A	G	607.03	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=29.63;RAW_MQ=45990.00;SOR=0.804	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,17:17:50:1|1:10012479_A_G:621,50,0
-20	10012498	.	C	G	481.02	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;QD=28.76;RAW_MQ=22302.00;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012479_A_G:495,33,0
-20	10012518	.	T	C	421.02	.	AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;QD=29.94;RAW_MQ=15102.00;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:30:1|1:10012479_A_G:435,30,0
-20	10012521	.	C	T	67.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.36;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.77;MQRankSum=-3.800e-02;QD=6.15;RAW_MQ=19192.00;ReadPosRankSum=1.97;SOR=1.179	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,224
-20	10012570	.	G	GCA	481.06	.	AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.55;QD=31.54;RAW_MQ=13361.00;SOR=3.056	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0
-20	10012572	.	GT	G	481.02	.	AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.52;QD=28.86;RAW_MQ=17802.00;SOR=3.442	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012570_G_GCA:495,33,0
-20	10012631	.	C	CG	514.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030e+00;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=47.53;MQRankSum=-1.670e+00;QD=24.51;RAW_MQ=49690.00;ReadPosRankSum=-8.350e-01;SOR=0.048	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297
-20	10012636	.	G	C	548.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=48.93;MQRankSum=-1.513e+00;QD=24.94;RAW_MQ=52665.00;ReadPosRankSum=-7.180e-01;SOR=0.058	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,14:22:99:0|1:10012631_C_CG:556,0,294
-20	10012714	.	G	C	1315.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.04;QD=29.41;RAW_MQ=98462.00;SOR=2.964	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1329,105,0
-20	10012751	.	T	C	952.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.56;QD=31.73;RAW_MQ=81069.00;SOR=0.976	GT:AD:DP:GQ:PL	1/1:0,30:30:89:966,89,0
-20	10013119	.	C	T	1032.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.72;ClippingRankSum=0.00;DP=59;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.48;MQRankSum=-1.089e+00;QD=17.50;RAW_MQ=156381.00;ReadPosRankSum=0.336;SOR=0.405	GT:AD:DP:GQ:PL	0/1:29,30:59:99:1040,0,936
-20	10013574	.	G	A	1071.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.47;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.09;MQRankSum=-2.710e-01;QD=15.53;RAW_MQ=236198.00;ReadPosRankSum=0.789;SOR=1.675	GT:AD:DP:GQ:PL	0/1:38,31:69:99:1079,0,1301
-20	10014990	.	C	CAT	1267.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=2.090;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=3.11;QD=16.68;RAW_MQ=321369.00;ReadPosRankSum=-3.430e-01;SOR=0.403	GT:AD:DP:GQ:PL	0/1:38,38:76:99:1275,0,1248
-20	10015679	.	C	T	161.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.16;RAW_MQ=39600.00;ReadPosRankSum=0.355;SOR=0.693	GT:AD:DP:GQ:PL	0/1:5,5:10:99:169,0,166
-20	10015761	.	T	C	365.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.982e+00;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQRankSum=1.29;QD=16.62;RAW_MQ=76441.00;ReadPosRankSum=-4.250e-01;SOR=0.352	GT:AD:DP:GQ:PL	0/1:9,13:22:99:373,0,284
-20	10018158	.	G	C	1660.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.21;ClippingRankSum=0.00;DP=89;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.12;QD=18.87;RAW_MQ=318169.00;ReadPosRankSum=0.516;SOR=0.834	GT:AD:DP:GQ:PL	0/1:40,48:88:99:1668,0,1165
-20	10018555	.	G	A	1588.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.270e-01;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.86;RAW_MQ=288000.00;ReadPosRankSum=0.463;SOR=0.627	GT:AD:DP:GQ:PL	0/1:35,45:80:99:1596,0,1211
-20	10019093	.	A	G	1265.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;ClippingRankSum=0.00;DP=69;ExcessHet=3.0103;FS=1.990;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=1.07;QD=18.34;RAW_MQ=245641.00;ReadPosRankSum=-2.300e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1273,0,1104
-20	10020229	.	G	A	1559.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.79;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.104;QD=19.02;RAW_MQ=290210.00;ReadPosRankSum=-3.680e-01;SOR=0.573	GT:AD:DP:GQ:PL	0/1:38,44:82:99:1567,0,1130
-20	10023689	.	G	A	1873.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.35;QD=23.42;RAW_MQ=285769.00;ReadPosRankSum=0.764;SOR=0.549	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1881,0,946
-20	10024107	.	C	T	1715.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.77;ClippingRankSum=0.00;DP=86;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.546e+00;QD=19.95;RAW_MQ=303563.00;ReadPosRankSum=0.329;SOR=0.823	GT:AD:DP:GQ:PL	0/1:38,48:86:99:1723,0,1086
-20	10024300	.	C	CTT	104.67	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.45;ClippingRankSum=0.00;DP=50;ExcessHet=3.0103;FS=6.107;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-6.000e-01;QD=9.52;RAW_MQ=134695.00;ReadPosRankSum=0.00;SOR=1.825	GT:AD:DP:GQ:PL	0/1:3,8:18:99:103,0,137
-20	10026357	.	T	C	1187.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700e+00;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.46;MQRankSum=-1.480e-01;QD=18.85;RAW_MQ=218717.00;ReadPosRankSum=-5.490e-01;SOR=0.722	GT:AD:DP:GQ:PL	0/1:28,35:63:99:1195,0,932
-20	10026794	.	C	T	1105.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.83;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=-7.190e-01;QD=21.26;RAW_MQ=191641.00;ReadPosRankSum=-7.000e-02;SOR=0.428	GT:AD:DP:GQ:PL	0/1:19,33:52:99:1113,0,529
-20	10027234	.	A	ATTAG	1350.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-8.450e-01;QD=19.57;RAW_MQ=236651.00;ReadPosRankSum=-9.310e-01;SOR=0.926	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1358,0,1964
-20	10027868	.	A	G	1760.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793e+00;ClippingRankSum=0.00;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.78;RAW_MQ=314882.00;ReadPosRankSum=1.23;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,45:89:99:0|1:10027868_A_G:1768,0,3201
-20	10027872	.	A	G	1745.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491e+00;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.54;RAW_MQ=300482.00;ReadPosRankSum=0.173;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136
-20	10028867	.	A	ATG	1136.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.740e-01;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=2.71;QD=16.01;RAW_MQ=338841.00;ReadPosRankSum=0.075;SOR=0.336	GT:AD:DP:GQ:PL	0/1:32,39:71:99:1144,0,916
-20	10030188	.	T	A	1393.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-1.013e+00;QD=17.20;RAW_MQ=288841.00;ReadPosRankSum=-1.072e+00;SOR=1.105	GT:AD:DP:GQ:PL	0/1:42,39:81:99:1401,0,1524
-20	10031254	.	A	AT	1493.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.100e-02;ClippingRankSum=0.00;DP=88;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.017;QD=17.57;RAW_MQ=313110.00;ReadPosRankSum=0.478;SOR=0.211	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1501,0,1159
-20	10031342	.	G	A	1855.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-8.660e-01;QD=19.95;RAW_MQ=332041.00;ReadPosRankSum=-2.630e-01;SOR=0.955	GT:AD:DP:GQ:PL	0/1:41,52:93:99:1863,0,1375
-20	10031798	.	G	A	4311.03	.	AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=31.11;RAW_MQ=369410.00;SOR=0.900	GT:AD:DP:GQ:PL	1/1:0,104:104:99:4325,313,0
-20	10031827	.	C	T	2025.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.55;ClippingRankSum=0.00;DP=108;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=-9.450e-01;QD=18.76;RAW_MQ=386569.00;ReadPosRankSum=-3.900e-01;SOR=0.382	GT:AD:DP:GQ:PL	0/1:52,56:108:99:2033,0,1798
-20	10032094	.	G	A	1241.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.49;ClippingRankSum=0.00;DP=84;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.96;RAW_MQ=302400.00;ReadPosRankSum=-4.640e-01;SOR=0.260	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1249,0,1497
-20	10032413	.	T	G	890.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142e+00;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-6.500e-02;QD=13.49;RAW_MQ=233138.00;ReadPosRankSum=-7.510e-01;SOR=1.293	GT:AD:DP:GQ:PL	0/1:35,31:66:99:898,0,1277
-20	10032882	.	A	T	1223.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697e+00;ClippingRankSum=0.00;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.014e+00;QD=16.31;RAW_MQ=267241.00;ReadPosRankSum=0.579;SOR=0.338	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1231,0,1406
-20	10032972	.	C	CAT	1152.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017e+00;QD=18.30;RAW_MQ=231241.00;ReadPosRankSum=-1.239e+00;SOR=1.300	GT:AD:DP:GQ:PL	0/1:33,30:63:99:1160,0,1477
-20	10034306	.	T	C	803.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661e+00;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.15;QD=10.71;RAW_MQ=272210.00;ReadPosRankSum=0.280;SOR=0.685	GT:AD:DP:GQ:PL	0/1:46,29:75:99:811,0,1593
-20	10036930	.	CGATAGCCCTAGCCCTAGATA	C	1066.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048e+00;QD=15.69;RAW_MQ=274847.00;ReadPosRankSum=0.200;SOR=0.269	GT:AD:DP:GQ:PL	0/1:39,29:68:99:1074,0,5571
-20	10037037	.	C	T	1457.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.50;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-1.193e+00;QD=18.00;RAW_MQ=293262.00;ReadPosRankSum=-1.694e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:39,42:81:99:1465,0,1124
-20	10037110	.	T	TGATA	2804.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=34.66;RAW_MQ=240219.00;SOR=1.022	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2818,189,0
-20	10037144	.	T	TGATAGATA	1847.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=29.40;RAW_MQ=187352.00;SOR=1.061	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1861,127,0
-20	10037709	.	A	T	1024.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.367e+00;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=0.934;QD=14.43;RAW_MQ=260041.00;ReadPosRankSum=0.600;SOR=0.608	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1032,0,1354
-20	10039371	.	T	G	1345.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.260e+00;ClippingRankSum=0.00;DP=74;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.18;RAW_MQ=266400.00;ReadPosRankSum=0.510;SOR=1.031	GT:AD:DP:GQ:PL	0/1:34,40:74:99:1353,0,1194
-20	10040772	.	C	CT	2019.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.69;QD=28.84;RAW_MQ=211048.00;SOR=0.811	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2033,210,0
-20	10040812	.	AT	A	2631.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;QD=36.76;RAW_MQ=203299.00;SOR=0.721	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2645,214,0
-20	10040821	.	T	A	1192.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.100e-02;ClippingRankSum=0.00;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=-9.700e-02;QD=15.29;RAW_MQ=199699.00;ReadPosRankSum=-1.410e+00;SOR=0.688	GT:AD:DP:GQ:PL	0/1:38,40:78:99:1200,0,1099
-20	10041304	.	C	T	2780.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.40;QD=30.54;RAW_MQ=247010.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2794,204,0
-20	10041701	.	A	ATATG	1433.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;ClippingRankSum=0.00;DP=78;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.90;MQRankSum=0.340;QD=25.60;RAW_MQ=270590.00;ReadPosRankSum=0.328;SOR=0.260	GT:AD:DP:GQ:PL	0/1:8,48:56:58:1441,0,58
-20	10042319	.	C	T	2673.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=21.53;RAW_MQ=229851.00;SOR=1.033	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2687,199,0
-20	10042761	.	A	G	3568.03	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.87;RAW_MQ=327600.00;SOR=1.389	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3582,272,0
-20	10042829	.	A	G	3070.03	.	AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;QD=31.04;RAW_MQ=278569.00;SOR=0.855	GT:AD:DP:GQ:PL	1/1:0,78:78:99:3084,235,0
-20	10043002	.	A	T	1308.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.99;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.22;RAW_MQ=313200.00;ReadPosRankSum=0.178;SOR=0.434	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1316,0,1659
-20	10044849	.	A	G	2106.03	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=27.86;RAW_MQ=213241.00;SOR=1.316	GT:AD:DP:GQ:PL	1/1:0,59:59:99:2120,177,0
-20	10045078	.	G	T	3286.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;QD=34.17;RAW_MQ=279389.00;SOR=0.876	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3300,244,0
-20	10045642	.	G	C	3122.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=28.60;RAW_MQ=286610.00;SOR=0.821	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3136,243,0
-20	10046178	.	AAGAAAGAAAG	A	2183.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.22;QD=25.57;RAW_MQ=144145.00;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2197,152,0
-20	10046537	.	A	G	840.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.909e+00;ClippingRankSum=0.00;DP=57;ExcessHet=3.0103;FS=3.724;MLEAC=1;MLEAF=0.500;MQ=54.50;MQRankSum=0.395;QD=14.75;RAW_MQ=169333.00;ReadPosRankSum=0.412;SOR=1.262	GT:AD:DP:GQ:PL	0/1:28,29:57:99:848,0,902
-20	10050828	.	T	C	1248.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.704e+00;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=2.887;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=0.892;QD=14.52;RAW_MQ=310441.00;ReadPosRankSum=0.073;SOR=0.521	GT:AD:DP:GQ:PL	0/1:49,37:86:99:1256,0,1768
-20	10051448	.	T	C	1155.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.010e-01;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=-1.404e+00;QD=16.51;RAW_MQ=247851.00;ReadPosRankSum=-5.490e-01;SOR=0.302	GT:AD:DP:GQ:PL	0/1:35,35:70:99:1163,0,1150
-20	10052688	.	C	A	1083.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.870;QD=14.07;RAW_MQ=274969.00;ReadPosRankSum=1.56;SOR=0.379	GT:AD:DP:GQ:PL	0/1:45,32:77:99:1091,0,1645
-20	10058022	.	T	C	996.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.346e+00;ClippingRankSum=0.00;DP=68;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=0.466;QD=14.66;RAW_MQ=237579.00;ReadPosRankSum=-4.530e-01;SOR=0.849	GT:AD:DP:GQ:PL	0/1:36,32:68:99:1004,0,1261
-20	10062935	.	C	CA	122.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.34;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.23;MQRankSum=-1.405e+00;QD=8.18;RAW_MQ=232368.00;ReadPosRankSum=-4.930e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:5,10:23:99:130,0,101
-20	10067049	.	TAAAAAAAA	T,TA	634.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.177;ClippingRankSum=0.00;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.41;MQRankSum=-3.420e-01;QD=33.11;RAW_MQ=204256.00;ReadPosRankSum=-4.960e-01;SOR=1.127	GT:AD:DP:GQ:PL	1/2:2,7,9:22:99:651,164,340,135,0,106
-20	10067090	.	C	A	2019.03	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=30.20;RAW_MQ=166789.00;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2033,164,0
-20	10067264	.	G	A	2937.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=30.49;RAW_MQ=257282.00;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0
-20	10067722	.	A	C	2161.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.67;RAW_MQ=198000.00;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
-20	10068158	.	GTGTATATATATA	G	96.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.520e-01;ClippingRankSum=0.00;DP=29;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=0.328;QD=13.80;RAW_MQ=93364.00;ReadPosRankSum=-2.530e-01;SOR=0.061	GT:AD:DP:GQ:PGT:PID:PL	0/1:3,4:7:57:0|1:10068158_GTGTATATATATA_G:104,0,57
-20	10068160	.	GTATATATATATGTA	G	36.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.660e-01;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQRankSum=-7.120e-01;QD=5.23;RAW_MQ=87005.00;ReadPosRankSum=0.967;SOR=1.802	GT:AD:DP:GQ:PGT:PID:PL	0/1:5,2:7:44:1|0:10068158_GTGTATATATATA_G:44,0,134
-20	10068981	.	G	A	2518.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.53;RAW_MQ=223200.00;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0
-20	10070602	.	T	C	2706.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.74;QD=32.63;RAW_MQ=255364.00;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
-20	10070936	.	T	A	3646.03	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;QD=30.36;RAW_MQ=279633.00;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10070936_T_A:3660,247,0
-20	10070938	.	G	GA	3680.06	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.10;QD=28.13;RAW_MQ=275964.00;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,79:79:99:1|1:10070936_T_A:3694,250,0
-20	10071135	.	C	T	3272.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=27.97;RAW_MQ=276123.00;SOR=1.003	GT:AD:DP:GQ:PL	1/1:0,79:79:99:3286,238,0
-20	10071187	.	G	A	3425.03	.	AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;QD=28.31;RAW_MQ=292441.00;SOR=1.367	GT:AD:DP:GQ:PL	1/1:0,82:82:99:3439,246,0
-20	10071890	.	T	C	1989.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=34.90;RAW_MQ=202969.00;SOR=0.728	GT:AD:DP:GQ:PL	1/1:0,57:57:99:2003,171,0
-20	10072505	.	A	G	2114.03	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.03;RAW_MQ=230400.00;SOR=0.822	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2128,191,0
-20	10074187	.	A	G	3116.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=35.21;RAW_MQ=276123.00;SOR=0.881	GT:AD:DP:GQ:PL	1/1:0,79:79:99:3130,238,0
-20	10074240	.	T	C	3421.03	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=35.18;RAW_MQ=307369.00;SOR=0.922	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3435,255,0
-20	10074716	.	G	A	2415.03	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;QD=29.59;RAW_MQ=232082.00;SOR=1.214	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2429,192,0
-20	10074806	.	G	A	2832.03	.	AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=32.25;RAW_MQ=250077.00;SOR=0.840	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2846,213,0
-20	10075043	.	T	C	2420.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.63;QD=34.86;RAW_MQ=220441.00;SOR=1.107	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2434,184,0
-20	10075168	.	C	T	3627.03	.	AC=2;AF=1.00;AN=2;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=32.49;RAW_MQ=309981.00;SOR=0.997	GT:AD:DP:GQ:PL	1/1:0,88:88:99:3641,264,0
-20	10075508	.	GA	G	1952.03	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.17;QD=27.89;RAW_MQ=288121.00;SOR=1.085	GT:AD:DP:GQ:PL	1/1:0,70:70:99:1966,210,0
-20	10076250	.	A	G	1128.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.386e+00;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=7.546;MLEAC=1;MLEAF=0.500;MQ=59.40;MQRankSum=-1.423e+00;QD=14.29;RAW_MQ=282266.00;ReadPosRankSum=-6.050e-01;SOR=0.344	GT:AD:DP:GQ:PL	0/1:40,39:79:99:1136,0,1339
-20	10076339	.	A	G	1330.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.900e-02;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=1.992;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=-8.660e-01;QD=18.48;RAW_MQ=256441.00;ReadPosRankSum=0.508;SOR=0.446	GT:AD:DP:GQ:PL	0/1:32,40:72:99:1338,0,1035
-20	10076399	.	G	A	1828.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.15;ClippingRankSum=0.00;DP=94;ExcessHet=3.0103;FS=1.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.45;RAW_MQ=338400.00;ReadPosRankSum=-8.630e-01;SOR=0.952	GT:AD:DP:GQ:PL	0/1:44,50:94:99:1836,0,1544
-20	10076989	.	CA	C,CAA	235.10	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-6.500e-01;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.16;MQRankSum=-4.630e-01;QD=8.71;RAW_MQ=257046.00;ReadPosRankSum=-1.960e-01;SOR=0.495	GT:AD:DP:GQ:PL	1/2:7,13,7:31:41:252,41,376,147,0,361
-20	10077752	.	T	C	1366.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.503e+00;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=4.458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.30;RAW_MQ=284400.00;ReadPosRankSum=-1.420e-01;SOR=1.251	GT:AD:DP:GQ:PL	0/1:34,45:79:99:1374,0,1187
-20	10079476	.	T	G	31.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.458e+00;ClippingRankSum=0.00;DP=44;ExcessHet=3.0103;FS=57.922;MLEAC=1;MLEAF=0.500;MQ=59.05;MQRankSum=-8.260e-01;QD=0.72;RAW_MQ=153410.00;ReadPosRankSum=-4.313e+00;SOR=4.970	GT:AD:DP:GQ:PL	0/1:33,11:44:39:39,0,1137
-20	10081750	.	C	A	1374.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.67;ClippingRankSum=0.00;DP=83;ExcessHet=3.0103;FS=0.824;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.56;RAW_MQ=298800.00;ReadPosRankSum=-6.260e-01;SOR=0.664	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1382,0,1525
-20	10081800	.	C	T	1130.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;ClippingRankSum=0.00;DP=68;ExcessHet=3.0103;FS=11.086;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.63;RAW_MQ=244800.00;ReadPosRankSum=-1.082e+00;SOR=0.143	GT:AD:DP:GQ:PL	0/1:35,33:68:99:1138,0,1222
-20	10082892	.	C	T	1727.03	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=29.05;RAW_MQ=155641.00;SOR=0.883	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,44:44:99:1|1:10082885_A_C:1741,132,0
-20	10085211	.	A	T	1231.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.501e+00;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=0.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=-1.028e+00;QD=16.21;RAW_MQ=272210.00;ReadPosRankSum=-2.800e-01;SOR=0.723	GT:AD:DP:GQ:PL	0/1:40,36:76:99:1239,0,1443
-20	10086110	.	G	A	1295.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.430e-01;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=1.810;MLEAC=1;MLEAF=0.500;MQ=59.14;MQRankSum=-6.800e-01;QD=16.00;RAW_MQ=283323.00;ReadPosRankSum=0.875;SOR=0.495	GT:AD:DP:GQ:PL	0/1:43,38:81:99:1303,0,1506
-20	10086283	.	G	T	1046.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.30;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=0.855;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.46;RAW_MQ=306000.00;ReadPosRankSum=1.61;SOR=0.529	GT:AD:DP:GQ:PL	0/1:52,32:84:99:1054,0,1771
-20	10086619	.	T	A	817.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.256;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=0.958;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.312e+00;QD=11.68;RAW_MQ=250610.00;ReadPosRankSum=-5.100e-02;SOR=0.846	GT:AD:DP:GQ:PL	0/1:45,25:70:99:825,0,1603
-20	10086853	.	G	A	1023.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.92;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-1.770e-01;QD=14.02;RAW_MQ=257810.00;ReadPosRankSum=-2.700e-01;SOR=0.767	GT:AD:DP:GQ:PL	0/1:41,32:73:99:1031,0,1280
-20	10086954	.	G	A	1116.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.61;ClippingRankSum=0.00;DP=68;ExcessHet=3.0103;FS=4.812;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.42;RAW_MQ=244800.00;ReadPosRankSum=-8.120e-01;SOR=1.185	GT:AD:DP:GQ:PL	0/1:34,34:68:99:1124,0,1051
-20	10087230	.	A	G	1863.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.407e+00;ClippingRankSum=0.00;DP=96;ExcessHet=3.0103;FS=3.860;MLEAC=1;MLEAF=0.500;MQ=58.88;MQRankSum=1.71;QD=19.41;RAW_MQ=332861.00;ReadPosRankSum=0.893;SOR=0.960	GT:AD:DP:GQ:PL	0/1:42,54:96:99:1871,0,1428
-20	10087394	.	T	G	1709.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.340e+00;ClippingRankSum=0.00;DP=84;ExcessHet=3.0103;FS=4.225;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=1.21;QD=20.35;RAW_MQ=299641.00;ReadPosRankSum=1.18;SOR=0.436	GT:AD:DP:GQ:PL	0/1:35,49:84:99:1717,0,1186
-20	10087754	.	T	G	1368.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=0.869;MLEAC=1;MLEAF=0.500;MQ=60.39;MQRankSum=2.19;QD=17.55;RAW_MQ=288141.00;ReadPosRankSum=-8.310e-01;SOR=0.562	GT:AD:DP:GQ:PL	0/1:37,41:78:99:1376,0,1239
-20	10087804	.	C	T	1640.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.94;ClippingRankSum=0.00;DP=100;ExcessHet=3.0103;FS=3.847;MLEAC=1;MLEAF=0.500;MQ=60.77;MQRankSum=2.62;QD=16.41;RAW_MQ=369310.00;ReadPosRankSum=1.02;SOR=0.369	GT:AD:DP:GQ:PL	0/1:50,50:100:99:1648,0,1511
-20	10087820	.	C	CAG	458.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.974e+00;ClippingRankSum=0.00;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.53;MQRankSum=0.422;QD=8.65;RAW_MQ=362700.00;ReadPosRankSum=-9.000e-03;SOR=0.850	GT:AD:DP:GQ:PL	0/1:35,18:53:99:466,0,1168
-20	10088063	.	C	T	1438.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.41;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=2.739;MLEAC=1;MLEAF=0.500;MQ=59.35;MQRankSum=0.515;QD=15.47;RAW_MQ=327579.00;ReadPosRankSum=0.354;SOR=1.053	GT:AD:DP:GQ:PL	0/1:49,44:93:99:1446,0,1403
-20	10088699	.	C	T	797.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=-3.140e+00;QD=12.86;RAW_MQ=199738.00;ReadPosRankSum=-5.770e-01;SOR=1.914	GT:AD:DP:GQ:PL	0/1:36,26:62:99:805,0,1088
-20	10088730	.	G	A	993.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.224;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=15.383;MLEAC=1;MLEAF=0.500;MQ=53.06;MQRankSum=-4.839e+00;QD=19.11;RAW_MQ=149199.00;ReadPosRankSum=0.433;SOR=1.592	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,23:52:99:0|1:10088730_G_A:1001,0,1152
-20	10088736	.	A	C	1102.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;ClippingRankSum=0.00;DP=56;ExcessHet=3.0103;FS=9.673;MLEAC=1;MLEAF=0.500;MQ=51.85;MQRankSum=-5.169e+00;QD=20.05;RAW_MQ=150523.00;ReadPosRankSum=-4.200e-02;SOR=0.851	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,27:55:99:0|1:10088730_G_A:1110,0,1194
-20	10088747	.	A	G	1132.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877e+00;ClippingRankSum=0.00;DP=56;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.25;MQRankSum=-4.907e+00;QD=20.97;RAW_MQ=147080.00;ReadPosRankSum=-3.390e-01;SOR=1.092	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,29:54:99:0|1:10088730_G_A:1140,0,995
-20	10088799	.	G	A	1039.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.50;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-2.498e+00;QD=19.62;RAW_MQ=150881.00;ReadPosRankSum=1.35;SOR=1.003	GT:AD:DP:GQ:PL	0/1:22,31:53:99:1047,0,617
-20	10088895	.	C	T	553.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;ClippingRankSum=0.00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.76;MQRankSum=0.577;QD=13.50;RAW_MQ=135291.00;ReadPosRankSum=0.907;SOR=0.653	GT:AD:DP:GQ:PL	0/1:23,18:41:99:561,0,673
-20	10088968	.	C	CAAA	1205.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.497;ClippingRankSum=0.00;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750e+00;QD=22.75;RAW_MQ=177808.00;ReadPosRankSum=1.02;SOR=1.012	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367
-20	10088980	.	T	C	1268.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585e+00;ClippingRankSum=0.00;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232e+00;QD=18.66;RAW_MQ=176353.00;ReadPosRankSum=0.999;SOR=0.709	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627
-20	10088985	.	T	C	1199.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920e-01;ClippingRankSum=0.00;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248e+00;QD=16.21;RAW_MQ=191764.00;ReadPosRankSum=1.38;SOR=0.742	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729
-20	10089441	.	A	G	1200.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-9.480e-01;QD=15.80;RAW_MQ=270841.00;ReadPosRankSum=0.161;SOR=1.363	GT:AD:DP:GQ:PL	0/1:37,39:76:99:1208,0,1313
-20	10089525	.	C	T	1569.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.86;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=1.53;QD=19.38;RAW_MQ=290210.00;ReadPosRankSum=0.428;SOR=0.617	GT:AD:DP:GQ:PL	0/1:38,43:81:99:1577,0,1088
-20	10090289	.	CA	C	414.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.39;QD=12.20;RAW_MQ=287682.00;ReadPosRankSum=-2.230e-01;SOR=0.859	GT:AD:DP:GQ:PL	0/1:14,20:38:99:422,0,230
-20	10090764	.	A	G	861.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659e+00;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.68;RAW_MQ=226800.00;ReadPosRankSum=0.695;SOR=0.310	GT:AD:DP:GQ:PL	0/1:34,29:63:99:869,0,1207
-20	10090970	.	T	C	1278.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.840e-01;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.51;QD=18.53;RAW_MQ=247538.00;ReadPosRankSum=0.429;SOR=0.518	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1286,0,1092
-20	10091214	.	C	T	1270.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-9.160e-01;QD=18.15;RAW_MQ=249769.00;ReadPosRankSum=0.392;SOR=0.625	GT:AD:DP:GQ:PL	0/1:33,37:70:99:1278,0,1110
-20	10092415	.	A	G	1656.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731e+00;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.40;RAW_MQ=367200.00;ReadPosRankSum=-7.000e-02;SOR=0.665	GT:AD:DP:GQ:PL	0/1:52,49:101:99:1664,0,1902
-20	10092927	.	G	T	127.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.507e+00;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-3.009e+00;QD=1.77;RAW_MQ=257282.00;ReadPosRankSum=-4.416e+00;SOR=5.279	GT:AD:DP:GQ:PL	0/1:59,13:72:99:135,0,1864
-20	10093568	.	GT	G	356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.426;ClippingRankSum=0.00;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=0.410;QD=10.49;RAW_MQ=203561.00;ReadPosRankSum=0.987;SOR=0.751	GT:AD:DP:GQ:PL	0/1:17,17:42:99:364,0,386
-20	10093923	.	T	A	1096.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.670e-01;ClippingRankSum=0.00;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=0.358;QD=16.37;RAW_MQ=234704.00;ReadPosRankSum=-2.256e+00;SOR=0.772	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1104,0,1257
-20	10094251	.	T	A	1291.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.83;RAW_MQ=226800.00;ReadPosRankSum=1.73;SOR=1.211	GT:AD:DP:GQ:PL	0/1:26,36:62:99:1299,0,781
-20	10094582	.	A	G	944.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388e+00;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=1.27;QD=13.69;RAW_MQ=254210.00;ReadPosRankSum=-5.270e-01;SOR=0.772	GT:AD:DP:GQ:PL	0/1:39,30:69:99:952,0,1350
-20	10094774	.	C	T	1057.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.840e-01;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.962;QD=14.10;RAW_MQ=274441.00;ReadPosRankSum=0.494;SOR=0.690	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1065,0,1282
-20	10095432	.	GTGATGATGA	G	869.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.27;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431e+00;QD=17.39;RAW_MQ=227748.00;ReadPosRankSum=0.660;SOR=0.460	GT:AD:DP:GQ:PL	0/1:27,23:50:99:877,0,2108
-20	10095741	.	A	G	1096.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.340e-01;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-2.313e+00;QD=15.67;RAW_MQ=237128.00;ReadPosRankSum=-3.260e-01;SOR=0.515	GT:AD:DP:GQ:PL	0/1:36,34:70:99:1104,0,1233
-20	10096293	.	C	T	1376.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.66;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQRankSum=1.40;QD=18.35;RAW_MQ=260861.00;ReadPosRankSum=0.012;SOR=0.638	GT:AD:DP:GQ:PL	0/1:37,38:75:99:1384,0,1258
-20	10096596	.	C	T	1583.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.612;QD=18.20;RAW_MQ=300461.00;ReadPosRankSum=0.166;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,47:87:99:1591,0,1273
-20	10096768	.	A	C	1703.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.764e+00;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=-1.609e+00;QD=18.72;RAW_MQ=319323.00;ReadPosRankSum=0.541;SOR=0.445	GT:AD:DP:GQ:PL	0/1:42,49:91:99:1711,0,1452
-20	10096899	.	G	T	1635.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.76;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=9.606;MLEAC=1;MLEAF=0.500;MQ=59.53;MQRankSum=-1.387e+00;QD=20.70;RAW_MQ=279938.00;ReadPosRankSum=0.378;SOR=1.707	GT:AD:DP:GQ:PGT:PID:PL	0/1:39,40:79:99:0|1:10096899_G_T:1643,0,1520
-20	10096905	.	TA	T	1630.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.550e-01;ClippingRankSum=0.00;DP=83;ExcessHet=3.0103;FS=11.159;MLEAC=1;MLEAF=0.500;MQ=59.27;MQRankSum=-1.677e+00;QD=19.65;RAW_MQ=291579.00;ReadPosRankSum=0.397;SOR=1.775	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,43:83:99:0|1:10096899_G_T:1638,0,1623
-20	10096933	.	G	C	1532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914e+00;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.802e+00;QD=18.03;RAW_MQ=298779.00;ReadPosRankSum=0.238;SOR=1.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770
-20	10096958	.	G	A	1787.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-1.701e+00;QD=19.43;RAW_MQ=323979.00;ReadPosRankSum=-1.860e+00;SOR=1.387	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629
-20	10097075	.	T	G	1466.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533e+00;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.389e+00;QD=15.94;RAW_MQ=315628.00;ReadPosRankSum=-2.850e-01;SOR=0.628	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482
-20	10097101	.	C	CTTT	1121.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=5.060;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-2.428e+00;QD=18.69;RAW_MQ=252294.00;ReadPosRankSum=1.11;SOR=0.277	GT:AD:DP:GQ:PL	0/1:34,26:64:99:1129,0,1306
-20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C	1084.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;ClippingRankSum=0.00;DP=89;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.27;MQRankSum=-6.464e+00;QD=12.19;RAW_MQ=262143.00;ReadPosRankSum=-3.231e+00;SOR=0.948	GT:AD:DP:GQ:PGT:PID:PL	0/1:57,32:89:99:0|1:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:1092,0,2241
-20	10097437	.	TTTTC	T	826.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=53.48;MQRankSum=4.88;QD=15.03;RAW_MQ=217330.00;ReadPosRankSum=2.93;SOR=1.382	GT:AD:DP:GQ:PGT:PID:PL	0/1:32,23:55:99:1|0:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:834,0,1193
-20	10097626	.	C	A	647.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.09;ClippingRankSum=0.00;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-1.331e+00;QD=13.49;RAW_MQ=162820.00;ReadPosRankSum=1.15;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957
-20	10097789	.	T	C	709.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157e+00;ClippingRankSum=0.00;DP=61;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=57.89;MQRankSum=-2.805e+00;QD=12.45;RAW_MQ=204439.00;ReadPosRankSum=-9.200e-02;SOR=0.756	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190
-20	10097928	.	G	A	591.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203e+00;ClippingRankSum=0.00;DP=40;ExcessHet=3.0103;FS=1.315;MLEAC=1;MLEAF=0.500;MQ=58.25;MQRankSum=-1.654e+00;QD=16.43;RAW_MQ=135723.00;ReadPosRankSum=0.057;SOR=0.951	GT:AD:DP:GQ:PL	0/1:17,19:36:99:599,0,586
-20	10098110	.	G	C	607.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=-1.477e+00;QD=16.88;RAW_MQ=124082.00;ReadPosRankSum=-7.140e-01;SOR=0.069	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,17:36:99:0|1:10098110_G_C:615,0,727
-20	10098135	.	C	A	492.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155e+00;ClippingRankSum=0.00;DP=38;ExcessHet=3.0103;FS=4.337;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=1.55;QD=12.96;RAW_MQ=135182.00;ReadPosRankSum=-7.690e-01;SOR=0.075	GT:AD:DP:GQ:PGT:PID:PL	0/1:24,14:38:99:0|1:10098110_G_C:500,0,964
-20	10098219	.	TATATATA	T	325.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.15;ClippingRankSum=0.00;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.94;MQRankSum=-2.050e-01;QD=15.50;RAW_MQ=65705.00;ReadPosRankSum=0.498;SOR=0.465	GT:AD:DP:GQ:PGT:PID:PL	0/1:12,9:21:99:0|1:10098219_TATATATA_T:333,0,461
-20	10098237	.	A	T	265.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.000e-03;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.40;MQRankSum=-1.742e+00;QD=20.43;RAW_MQ=37064.00;ReadPosRankSum=0.277;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273
-20	10098265	.	T	C	154.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;ClippingRankSum=0.00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834e+00;QD=25.77;RAW_MQ=10564.00;ReadPosRankSum=0.00;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59
-20	10098885	.	C	CA	463.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.89;MQRankSum=-4.449e+00;QD=14.96;RAW_MQ=77157.00;ReadPosRankSum=-1.590e-01;SOR=0.518	GT:AD:DP:GQ:PL	0/1:17,14:31:99:471,0,572
-20	10098945	.	T	C	473.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.504e+00;QD=21.53;RAW_MQ=57553.00;ReadPosRankSum=0.837;SOR=2.368	GT:AD:DP:GQ:PL	0/1:9,13:22:99:481,0,248
-20	10098987	.	C	T	400.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.13;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.88;MQRankSum=-2.734e+00;QD=16.69;RAW_MQ=64586.00;ReadPosRankSum=0.348;SOR=2.925	GT:AD:DP:GQ:PL	0/1:11,13:24:99:408,0,350
-20	10099029	.	T	C	355.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.809e+00;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=2.032;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641e+00;QD=12.70;RAW_MQ=79617.00;ReadPosRankSum=-7.930e-01;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
-20	10099034	.	C	A	355.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.76;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=4.265;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641e+00;QD=12.70;RAW_MQ=79617.00;ReadPosRankSum=-1.540e+00;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
-20	10099044	.	A	C	355.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148e+00;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418e+00;QD=14.82;RAW_MQ=59851.00;ReadPosRankSum=-2.625e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:363,0,768
-20	10099046	.	T	C	325.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165e+00;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418e+00;QD=13.57;RAW_MQ=59851.00;ReadPosRankSum=-2.686e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:333,0,603
-20	10099055	.	T	C	277.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554e+00;ClippingRankSum=0.00;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.46;MQRankSum=-4.316e+00;QD=12.07;RAW_MQ=58555.00;ReadPosRankSum=-2.131e+00;SOR=0.665	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,8:23:99:0|1:10099029_T_C:285,0,673
-20	10099079	.	C	T	137.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=0.00;DP=29;ExcessHet=3.0103;FS=1.862;MLEAC=1;MLEAF=0.500;MQ=52.09;MQRankSum=-2.821e+00;QD=4.74;RAW_MQ=78698.00;ReadPosRankSum=1.97;SOR=1.289	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,6:29:99:0|1:10099029_T_C:145,0,886
-20	10099111	.	T	TTTTGTTTG	686.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.207e+00;ClippingRankSum=0.00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.12;MQRankSum=-4.071e+00;QD=19.62;RAW_MQ=109737.00;ReadPosRankSum=-1.200e-01;SOR=0.511	GT:AD:DP:GQ:PL	0/1:22,13:35:99:694,0,802
-20	10099140	.	G	T	1026.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140e-01;ClippingRankSum=0.00;DP=62;ExcessHet=3.0103;FS=2.241;MLEAC=1;MLEAF=0.500;MQ=55.72;MQRankSum=-2.469e+00;QD=16.56;RAW_MQ=192512.00;ReadPosRankSum=0.169;SOR=1.114	GT:AD:DP:GQ:PL	0/1:30,32:62:99:1034,0,931
-20	10099190	.	G	T	1055.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-02;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQRankSum=-1.711e+00;QD=16.24;RAW_MQ=220251.00;ReadPosRankSum=-1.418e+00;SOR=0.776	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1063,0,1154
-20	10099220	.	A	G	598.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.664e+00;ClippingRankSum=0.00;DP=45;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-2.596e+00;QD=13.30;RAW_MQ=149477.00;ReadPosRankSum=0.331;SOR=0.519	GT:AD:DP:GQ:PL	0/1:25,20:45:99:606,0,873
-20	10099250	.	G	A	720.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.17;ClippingRankSum=0.00;DP=37;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.71;MQRankSum=-2.272e+00;QD=19.48;RAW_MQ=119006.00;ReadPosRankSum=0.169;SOR=0.162	GT:AD:DP:GQ:PL	0/1:16,21:37:99:728,0,424
-20	10099535	.	G	A	1356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.03;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=2.172;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-1.418e+00;QD=20.87;RAW_MQ=226251.00;ReadPosRankSum=-5.080e-01;SOR=0.408	GT:AD:DP:GQ:PL	0/1:26,39:65:99:1364,0,686
-20	10099565	.	C	T	1367.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.60;ClippingRankSum=0.00;DP=69;ExcessHet=3.0103;FS=8.736;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-1.266e+00;QD=19.82;RAW_MQ=243410.00;ReadPosRankSum=0.740;SOR=0.191	GT:AD:DP:GQ:PL	0/1:31,38:69:99:1375,0,994
-20	10099755	.	C	T	1119.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.55;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=2.074;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-2.200e-02;QD=17.22;RAW_MQ=232610.00;ReadPosRankSum=-6.840e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1127,0,1148
-20	10099832	.	A	G	1094.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.563e+00;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=4.632;MLEAC=1;MLEAF=0.500;MQ=58.96;MQRankSum=0.869;QD=15.20;RAW_MQ=250276.00;ReadPosRankSum=0.213;SOR=0.871	GT:AD:DP:GQ:PL	0/1:39,33:72:99:1102,0,1430
+20	10000117	.	C	T	926.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.913;PG=5;QD=14.48;RAW_MQ=228169.00;ReadPosRankSum=-1.790e-01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
+20	10000211	.	C	T	962.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.06;PG=5;QD=18.16;RAW_MQ=192169.00;ReadPosRankSum=1.07;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
+20	10000439	.	T	G	2819.06	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;PG=13;QD=25.36;RAW_MQ=279076.00;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,80:80:99:2833,240,0
+20	10000598	.	T	A	1956.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;PG=13;QD=28.73;RAW_MQ=149628.00;SOR=1.225	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1970,147,0
+20	10000694	.	G	A	1029.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.60;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.66;MQRankSum=-5.114e+00;PG=5;QD=12.56;RAW_MQ=194196.00;ReadPosRankSum=0.182;SOR=0.566	GT:AD:DP:GQ:PL	0/1:45,37:82:99:1037,0,1601
+20	10000758	.	T	A	3853.06	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;PG=12;QD=30.97;RAW_MQ=270581.00;SOR=0.802	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3867,286,0
+20	10001019	.	T	G	671.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.541e+00;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=3.406;MLEAC=1;MLEAF=0.500;MQ=49.49;MQRankSum=-7.498e+00;PG=3;QD=10.33;RAW_MQ=159195.00;ReadPosRankSum=-1.497e+00;SOR=0.665	GT:AD:DP:GQ:PL	0/1:39,26:65:99:679,0,1426
+20	10001298	.	T	A	2932.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;PG=13;QD=27.24;RAW_MQ=218493.00;SOR=0.963	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2946,220,0
+20	10001436	.	A	AAGGCT	2325.03	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.88;PG=11;QD=28.20;RAW_MQ=93596.00;SOR=3.442	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2339,156,0
+20	10001474	.	C	T	2655.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;PG=12;QD=25.00;RAW_MQ=141456.00;SOR=1.516	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2669,219,0
+20	10001617	.	C	A	1752.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.26;ClippingRankSum=0.00;DP=103;ExcessHet=3.0103;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=1.37;PG=5;QD=17.02;RAW_MQ=358589.00;ReadPosRankSum=-5.780e-01;SOR=1.346	GT:AD:DP:GQ:PL	0/1:52,51:103:99:1760,0,1781
+20	10001628	.	G	A	3913.06	.	AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;PG=13;QD=29.56;RAW_MQ=332548.00;SOR=1.053	GT:AD:DP:GQ:PL	1/1:0,95:95:99:3927,285,0
+20	10001661	.	T	C	3621.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;PG=13;QD=30.62;RAW_MQ=275574.00;SOR=1.193	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0
+20	10001670	.	T	G	3688.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;PG=13;QD=28.17;RAW_MQ=267297.00;SOR=0.995	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0
+20	10002058	.	T	G	2978.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.00;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;MQRankSum=3.07;PG=13;QD=26.80;RAW_MQ=250206.00;ReadPosRankSum=-5.240e-01;SOR=0.776	GT:AD:DP:GQ:PL	1/1:1,74:75:99:2992,216,0
+20	10002099	.	C	T	1215.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820e-01;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-8.500e-01;PG=0;QD=18.70;RAW_MQ=209529.00;ReadPosRankSum=-3.600e-01;SOR=0.375	GT:AD:DP:GQ:PL	0/1:27,38:65:99:1223,0,844
+20	10002138	.	C	G	2458.06	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.38;PG=12;QD=26.00;RAW_MQ=168463.00;SOR=0.730	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0
+20	10002142	.	G	C	2422.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.31;PG=12;QD=30.02;RAW_MQ=164863.00;SOR=0.853	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,52:52:99:1|1:10002138_C_G:2436,166,0
+20	10002458	.	G	GTTT	2154.96	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.07;PG=0;QD=31.98;RAW_MQ=127415.00;SOR=2.049	GT:AD:DP:GQ:PL	1/1:0,6:16:99:2090,167,0
+20	10002470	.	C	T	2537.06	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;PG=12;QD=27.51;RAW_MQ=144226.00;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2551,189,0
+20	10002625	.	G	T	2680.06	.	AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;PG=12;QD=29.11;RAW_MQ=223179.00;SOR=1.127	GT:AD:DP:GQ:PL	1/1:0,64:64:99:2694,193,0
+20	10003021	.	C	T	2398.06	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;PG=13;QD=28.08;RAW_MQ=208779.00;SOR=1.071	GT:AD:DP:GQ:PL	1/1:0,60:60:99:2412,181,0
+20	10003358	.	A	C	1475.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.000e-03;ClippingRankSum=0.00;DP=90;ExcessHet=3.0103;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.01;PG=5;QD=16.58;RAW_MQ=321769.00;ReadPosRankSum=-4.440e-01;SOR=0.572	GT:AD:DP:GQ:PL	0/1:45,44:89:99:1483,0,1477
+20	10003651	.	T	C	3635.06	.	AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;PG=13;QD=23.23;RAW_MQ=325876.00;SOR=1.511	GT:AD:DP:GQ:PL	1/1:0,93:93:99:3649,279,0
+20	10003692	.	A	G	2624.06	.	AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;PG=13;QD=29.03;RAW_MQ=240338.00;SOR=1.352	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2638,205,0
+20	10003832	.	G	A	2720.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;PG=13;QD=30.67;RAW_MQ=215436.00;SOR=1.473	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2734,199,0
+20	10004094	.	A	C	1840.06	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;PG=13;QD=34.72;RAW_MQ=147492.00;SOR=1.524	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1854,157,0
+20	10004147	.	A	G	1852.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;PG=12;QD=26.61;RAW_MQ=157262.00;SOR=1.136	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1866,156,0
+20	10004193	.	G	T	939.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.040e-01;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=2.391;MLEAC=1;MLEAF=0.500;MQ=59.32;MQRankSum=3.42;PG=0;QD=18.07;RAW_MQ=186469.00;ReadPosRankSum=0.775;SOR=1.019	GT:AD:DP:GQ:PL	0/1:23,29:52:99:947,0,775
+20	10004222	.	C	CA	42.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;ClippingRankSum=0.00;DP=55;ExcessHet=3.0103;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.05;MQRankSum=-2.042e+00;PG=0;QD=1.09;RAW_MQ=198329.00;ReadPosRankSum=-5.200e-02;SOR=0.434	GT:AD:DP:GQ:PL	0/1:31,8:39:50:50,0,923
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+20	10004389	.	T	G	2509.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;PG=13;QD=28.55;RAW_MQ=199570.00;SOR=1.143	GT:AD:DP:GQ:PL	1/1:0,62:62:99:2523,187,0
+20	10004610	.	A	C	3640.06	.	AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;PG=13;QD=34.42;RAW_MQ=306605.00;SOR=0.761	GT:AD:DP:GQ:PL	1/1:0,89:89:99:3654,267,0
+20	10004725	.	A	G	972.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.154e+00;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=15.830;MLEAC=1;MLEAF=0.500;MQ=55.27;MQRankSum=3.01;PG=0;QD=14.96;RAW_MQ=198562.00;ReadPosRankSum=1.79;SOR=0.605	GT:AD:DP:GQ:PL	0/1:35,30:65:99:980,0,1168
+20	10004769	.	TAAAACTATGC	T	1011.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.60;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.37;MQRankSum=-6.625e+00;PG=0;QD=15.81;RAW_MQ=216626.00;ReadPosRankSum=2.22;SOR=1.306	GT:AD:DP:GQ:PL	0/1:37,27:64:99:1019,0,1471
+20	10004874	.	A	C	3617.06	.	AC=2;AF=1.00;AN=2;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;PG=20;QD=28.53;RAW_MQ=306223.00;SOR=1.286	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0
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+20	10005587	.	A	G	1250.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.340e-01;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-9.720e-01;PG=5;QD=17.37;RAW_MQ=257810.00;ReadPosRankSum=0.649;SOR=0.848	GT:AD:DP:GQ:PL	0/1:36,36:72:99:1258,0,1236
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+20	10006819	.	AAAAC	A	2555.03	.	AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.13;PG=11;QD=33.27;RAW_MQ=284000.00;SOR=0.762	GT:AD:DP:GQ:PL	1/1:0,58:58:99:2569,176,0
+20	10007150	.	G	C	690.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.476e+00;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=5.048;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=10.96;RAW_MQ=226800.00;ReadPosRankSum=-1.745e+00;SOR=0.746	GT:AD:DP:GQ:PGT:PID:PL	0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479
+20	10007175	.	C	T	1371.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;ClippingRankSum=0.00;DP=61;ExcessHet=3.0103;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=1.32;PG=1;QD=22.49;RAW_MQ=216841.00;ReadPosRankSum=-7.300e-01;SOR=0.434	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780
+20	10007352	.	C	T	2779.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;PG=13;QD=31.26;RAW_MQ=249241.00;SOR=1.054	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2793,208,0
+20	10007531	.	A	G	2935.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;PG=13;QD=27.76;RAW_MQ=260569.00;SOR=1.577	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2949,217,0
+20	10007980	.	A	C	3539.06	.	AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;PG=12;QD=29.09;RAW_MQ=331800.00;SOR=0.990	GT:AD:DP:GQ:PL	1/1:0,90:90:99:3553,270,0
+20	10008029	.	T	TA	2010.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;ClippingRankSum=0.00;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.98;MQRankSum=0.576;PG=9;QD=26.80;RAW_MQ=327251.00;ReadPosRankSum=-1.055e+00;SOR=0.788	GT:AD:DP:GQ:PL	1/1:3,72:75:99:2024,145,0
+20	10008146	.	TA	T	2165.03	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.59;PG=13;QD=30.93;RAW_MQ=268000.00;SOR=0.874	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2179,211,0
+20	10008221	.	T	C	3239.06	.	AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;PG=13;QD=26.08;RAW_MQ=289669.00;SOR=0.850	GT:AD:DP:GQ:PL	1/1:0,80:80:99:3253,240,0
+20	10008458	.	T	G	2669.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.54;PG=13;QD=33.85;RAW_MQ=193211.00;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,69:69:99:2683,207,0
+20	10008742	.	G	T	736.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.89;ClippingRankSum=0.00;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.502e+00;PG=0;QD=15.03;RAW_MQ=67874.00;ReadPosRankSum=0.772;SOR=0.741	GT:AD:DP:GQ:PL	0/1:23,26:49:99:744,0,580
+20	10008758	.	C	CA	707.49	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;ClippingRankSum=0.00;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-1.168e+00;PG=3;QD=20.21;RAW_MQ=54656.00;ReadPosRankSum=-2.340e-01;SOR=0.249	GT:AD:DP:GQ:PL	1/1:4,31:35:10:721,10,0
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+20	10008948	.	TA	T	2081.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.30;MQRankSum=2.05;PG=12;QD=27.08;RAW_MQ=139463.00;ReadPosRankSum=0.749;SOR=0.818	GT:AD:DP:GQ:PGT:PID:PL	1/1:1,50:51:99:1|1:10008921_C_CA:2095,107,0
+20	10008952	.	CACACACACACA	C,CCACACACACA	1687.02	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.941;ClippingRankSum=0.00;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.81;MQRankSum=1.84;PG=0;QD=25.42;RAW_MQ=154909.00;ReadPosRankSum=0.685;SOR=1.127	GT:AD:DP:GQ:PL	1/2:1,14,11:34:99:1704,525,845,582,0,530
+20	10009227	.	A	G	1390.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220e+00;ClippingRankSum=0.00;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.43;PG=0;QD=22.43;RAW_MQ=202588.00;ReadPosRankSum=-1.093e+00;SOR=0.281	GT:AD:DP:GQ:PL	0/1:23,39:62:99:1398,0,740
+20	10009246	.	A	G	3017.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;PG=20;QD=27.65;RAW_MQ=242208.00;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,77:77:99:3031,231,0
+20	10009400	.	T	A	3013.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=13;QD=29.48;RAW_MQ=266400.00;SOR=0.804	GT:AD:DP:GQ:PL	1/1:0,74:74:99:3027,223,0
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+20	10009842	.	G	GAA	562.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.872;ClippingRankSum=0.00;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQRankSum=-6.030e-01;PG=0;QD=16.55;RAW_MQ=150092.00;ReadPosRankSum=0.052;SOR=0.738	GT:AD:DP:GQ:PL	0/1:19,15:34:99:570,0,690
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+20	10009879	.	A	G	2259.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.53;ClippingRankSum=0.00;DP=50;ExcessHet=3.0103;FS=9.369;MLEAC=2;MLEAF=1.00;MQ=49.85;MQRankSum=1.57;PG=2;QD=32.62;RAW_MQ=124261.00;ReadPosRankSum=1.39;SOR=1.474	GT:AD:DP:GQ:PL	1/1:2,47:49:99:2273,150,0
+20	10009883	.	A	G	2166.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.56;PG=7;QD=29.33;RAW_MQ=132938.00;SOR=1.659	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2180,147,0
+20	10010393	.	T	G	1485.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.351e+00;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=11.600;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-1.284e+00;PG=0;QD=18.81;RAW_MQ=278882.00;ReadPosRankSum=-1.630e+00;SOR=0.606	GT:AD:DP:GQ:PL	0/1:36,43:79:99:1493,0,1230
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+20	10010766	.	T	G	2426.06	.	AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=13;QD=35.36;RAW_MQ=241200.00;SOR=0.818	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2440,199,0
+20	10010832	.	T	C	2966.06	.	AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;PG=13;QD=34.30;RAW_MQ=265538.00;SOR=1.091	GT:AD:DP:GQ:PL	1/1:0,75:75:99:2980,226,0
+20	10011075	.	C	T	1346.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.36;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=4;QD=16.22;RAW_MQ=306000.00;ReadPosRankSum=-1.057e+00;SOR=0.968	GT:AD:DP:GQ:PL	0/1:44,39:83:99:1354,0,1333
+20	10011309	.	T	C	2707.06	.	AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=13;QD=27.00;RAW_MQ=277200.00;SOR=1.223	GT:AD:DP:GQ:PL	1/1:0,77:77:99:2721,231,0
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+20	10012021	.	CA	C	1999.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;PG=13;QD=30.29;RAW_MQ=228076.00;SOR=1.196	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2013,198,0
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+20	10012384	.	T	C	250.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.773e+00;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=7.375;MLEAC=1;MLEAF=0.500;MQ=53.75;MQRankSum=-8.110e-01;PG=3;QD=13.92;RAW_MQ=54886.00;ReadPosRankSum=0.190;SOR=0.044	GT:AD:DP:GQ:PL	0/1:10,8:18:99:258,0,355
+20	10012387	.	T	C	548.06	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.96;PG=11;QD=34.25;RAW_MQ=47686.00;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,16:16:50:562,50,0
+20	10012479	.	A	G	607.06	.	AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;PG=11;QD=29.63;RAW_MQ=45990.00;SOR=0.804	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,17:17:50:1|1:10012479_A_G:621,50,0
+20	10012498	.	C	G	481.06	.	AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;PG=12;QD=28.76;RAW_MQ=22302.00;SOR=1.270	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,11:11:33:1|1:10012479_A_G:495,33,0
+20	10012518	.	T	C	421.06	.	AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;PG=10;QD=29.94;RAW_MQ=15102.00;SOR=0.892	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:30:1|1:10012479_A_G:435,30,0
+20	10012521	.	C	T	67.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.36;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.77;MQRankSum=-3.800e-02;PG=4;QD=6.15;RAW_MQ=19192.00;ReadPosRankSum=1.97;SOR=1.179	GT:AD:DP:GQ:PL	0/1:8,3:11:75:75,0,224
+20	10012570	.	G	GCA	481.02	.	AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.55;PG=10;QD=31.54;RAW_MQ=13361.00;SOR=3.056	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0
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+20	10012631	.	C	CG	514.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030e+00;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=8.822;MLEAC=1;MLEAF=0.500;MQ=47.53;MQRankSum=-1.670e+00;PG=0;QD=24.50;RAW_MQ=49690.00;ReadPosRankSum=-8.350e-01;SOR=0.048	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297
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+20	10013119	.	C	T	1032.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.72;ClippingRankSum=0.00;DP=59;ExcessHet=3.0103;FS=2.248;MLEAC=1;MLEAF=0.500;MQ=51.48;MQRankSum=-1.089e+00;PG=0;QD=17.50;RAW_MQ=156381.00;ReadPosRankSum=0.336;SOR=0.405	GT:AD:DP:GQ:PL	0/1:29,30:59:99:1040,0,936
+20	10013574	.	G	A	1071.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.47;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=7.109;MLEAC=1;MLEAF=0.500;MQ=58.09;MQRankSum=-2.710e-01;PG=4;QD=15.53;RAW_MQ=236198.00;ReadPosRankSum=0.789;SOR=1.675	GT:AD:DP:GQ:PL	0/1:38,31:69:99:1079,0,1301
+20	10014990	.	C	CAT	1267.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=2.090;MLEAC=1;MLEAF=0.500;MQ=60.78;MQRankSum=3.11;PG=5;QD=16.68;RAW_MQ=321369.00;ReadPosRankSum=-3.430e-01;SOR=0.403	GT:AD:DP:GQ:PL	0/1:38,38:76:99:1275,0,1248
+20	10015679	.	C	T	161.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=16.16;RAW_MQ=39600.00;ReadPosRankSum=0.355;SOR=0.693	GT:AD:DP:GQ:PL	0/1:5,5:10:99:169,0,166
+20	10015761	.	T	C	365.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.982e+00;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQRankSum=1.29;PG=4;QD=16.62;RAW_MQ=76441.00;ReadPosRankSum=-4.250e-01;SOR=0.352	GT:AD:DP:GQ:PL	0/1:9,13:22:99:373,0,284
+20	10018158	.	G	C	1660.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.21;ClippingRankSum=0.00;DP=89;ExcessHet=3.0103;FS=0.808;MLEAC=1;MLEAF=0.500;MQ=59.79;MQRankSum=1.12;PG=4;QD=18.87;RAW_MQ=318169.00;ReadPosRankSum=0.516;SOR=0.834	GT:AD:DP:GQ:PL	0/1:40,48:88:99:1668,0,1165
+20	10018555	.	G	A	1588.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.270e-01;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=4.241;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=19.86;RAW_MQ=288000.00;ReadPosRankSum=0.463;SOR=0.627	GT:AD:DP:GQ:PL	0/1:35,45:80:99:1596,0,1211
+20	10019093	.	A	G	1265.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;ClippingRankSum=0.00;DP=69;ExcessHet=3.0103;FS=1.990;MLEAC=1;MLEAF=0.500;MQ=59.67;MQRankSum=1.07;PG=4;QD=18.34;RAW_MQ=245641.00;ReadPosRankSum=-2.300e-01;SOR=0.665	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1273,0,1104
+20	10020229	.	G	A	1559.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.79;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=0.833;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.104;PG=0;QD=19.02;RAW_MQ=290210.00;ReadPosRankSum=-3.680e-01;SOR=0.573	GT:AD:DP:GQ:PL	0/1:38,44:82:99:1567,0,1130
+20	10023689	.	G	A	1873.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=0.877;MLEAC=1;MLEAF=0.500;MQ=59.77;MQRankSum=1.35;PG=0;QD=23.42;RAW_MQ=285769.00;ReadPosRankSum=0.764;SOR=0.549	GT:AD:DP:GQ:PL	0/1:29,51:80:99:1881,0,946
+20	10024107	.	C	T	1715.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.77;ClippingRankSum=0.00;DP=86;ExcessHet=3.0103;FS=0.817;MLEAC=1;MLEAF=0.500;MQ=59.41;MQRankSum=-1.546e+00;PG=0;QD=19.95;RAW_MQ=303563.00;ReadPosRankSum=0.329;SOR=0.823	GT:AD:DP:GQ:PL	0/1:38,48:86:99:1723,0,1086
+20	10024300	.	C	CTT	104.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.45;ClippingRankSum=0.00;DP=50;ExcessHet=3.0103;FS=6.107;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-6.000e-01;PG=0;QD=9.51;RAW_MQ=134695.00;ReadPosRankSum=0.00;SOR=1.825	GT:AD:DP:GQ:PL	0/1:3,8:18:99:103,0,137
+20	10026357	.	T	C	1187.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700e+00;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.46;MQRankSum=-1.480e-01;PG=0;QD=18.85;RAW_MQ=218717.00;ReadPosRankSum=-5.490e-01;SOR=0.722	GT:AD:DP:GQ:PL	0/1:28,35:63:99:1195,0,932
+20	10026794	.	C	T	1105.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.83;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.57;MQRankSum=-7.190e-01;PG=0;QD=21.26;RAW_MQ=191641.00;ReadPosRankSum=-7.000e-02;SOR=0.428	GT:AD:DP:GQ:PL	0/1:19,33:52:99:1113,0,529
+20	10027234	.	A	ATTAG	1350.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-8.450e-01;PG=4;QD=19.57;RAW_MQ=236651.00;ReadPosRankSum=-9.310e-01;SOR=0.926	GT:AD:DP:GQ:PL	0/1:34,35:69:99:1358,0,1964
+20	10027868	.	A	G	1760.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793e+00;ClippingRankSum=0.00;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;PG=0;QD=19.78;RAW_MQ=314882.00;ReadPosRankSum=1.23;SOR=0.881	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,45:89:99:0|1:10027868_A_G:1768,0,3201
+20	10027872	.	A	G	1745.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491e+00;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;PG=0;QD=20.54;RAW_MQ=300482.00;ReadPosRankSum=0.173;SOR=0.826	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136
+20	10028867	.	A	ATG	1136.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.740e-01;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=2.71;PG=0;QD=16.01;RAW_MQ=338841.00;ReadPosRankSum=0.075;SOR=0.336	GT:AD:DP:GQ:PL	0/1:32,39:71:99:1144,0,916
+20	10030188	.	T	A	1393.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-1.013e+00;PG=0;QD=17.21;RAW_MQ=288841.00;ReadPosRankSum=-1.072e+00;SOR=1.105	GT:AD:DP:GQ:PL	0/1:42,39:81:99:1401,0,1524
+20	10031254	.	A	AT	1493.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.100e-02;ClippingRankSum=0.00;DP=88;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=0.017;PG=0;QD=17.57;RAW_MQ=313110.00;ReadPosRankSum=0.478;SOR=0.211	GT:AD:DP:GQ:PL	0/1:38,47:85:99:1501,0,1159
+20	10031342	.	G	A	1855.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=1.714;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-8.660e-01;PG=4;QD=19.95;RAW_MQ=332041.00;ReadPosRankSum=-2.630e-01;SOR=0.955	GT:AD:DP:GQ:PL	0/1:41,52:93:99:1863,0,1375
+20	10031798	.	G	A	4311.06	.	AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;PG=43;QD=31.11;RAW_MQ=369410.00;SOR=0.900	GT:AD:DP:GQ:PL	1/1:0,104:104:99:4325,313,0
+20	10031827	.	C	T	2025.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.55;ClippingRankSum=0.00;DP=108;ExcessHet=3.0103;FS=4.729;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=-9.450e-01;PG=0;QD=18.76;RAW_MQ=386569.00;ReadPosRankSum=-3.900e-01;SOR=0.382	GT:AD:DP:GQ:PL	0/1:52,56:108:99:2033,0,1798
+20	10032094	.	G	A	1241.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.49;ClippingRankSum=0.00;DP=84;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=14.96;RAW_MQ=302400.00;ReadPosRankSum=-4.640e-01;SOR=0.260	GT:AD:DP:GQ:PL	0/1:47,36:83:99:1249,0,1497
+20	10032413	.	T	G	890.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142e+00;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-6.500e-02;PG=0;QD=13.49;RAW_MQ=233138.00;ReadPosRankSum=-7.510e-01;SOR=1.293	GT:AD:DP:GQ:PL	0/1:35,31:66:99:898,0,1277
+20	10032882	.	A	T	1223.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697e+00;ClippingRankSum=0.00;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.014e+00;PG=5;QD=16.32;RAW_MQ=267241.00;ReadPosRankSum=0.579;SOR=0.338	GT:AD:DP:GQ:PL	0/1:39,36:75:99:1231,0,1406
+20	10032972	.	C	CAT	1152.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017e+00;PG=5;QD=18.30;RAW_MQ=231241.00;ReadPosRankSum=-1.239e+00;SOR=1.300	GT:AD:DP:GQ:PL	0/1:33,30:63:99:1160,0,1477
+20	10034306	.	T	C	803.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661e+00;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.15;PG=0;QD=10.72;RAW_MQ=272210.00;ReadPosRankSum=0.280;SOR=0.685	GT:AD:DP:GQ:PL	0/1:46,29:75:99:811,0,1593
+20	10036930	.	CGATAGCCCTAGCCCTAGATA	C	1066.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048e+00;PG=0;QD=15.69;RAW_MQ=274847.00;ReadPosRankSum=0.200;SOR=0.269	GT:AD:DP:GQ:PL	0/1:39,29:68:99:1074,0,5571
+20	10037037	.	C	T	1457.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.50;ClippingRankSum=0.00;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-1.193e+00;PG=0;QD=18.00;RAW_MQ=293262.00;ReadPosRankSum=-1.694e+00;SOR=0.495	GT:AD:DP:GQ:PL	0/1:39,42:81:99:1465,0,1124
+20	10037110	.	T	TGATA	2804.03	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;PG=5;QD=34.66;RAW_MQ=240219.00;SOR=1.022	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2818,189,0
+20	10037144	.	T	TGATAGATA	1847.03	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;PG=0;QD=29.40;RAW_MQ=187352.00;SOR=1.061	GT:AD:DP:GQ:PL	1/1:0,36:36:99:1861,127,0
+20	10037709	.	A	T	1024.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.367e+00;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQRankSum=0.934;PG=0;QD=14.43;RAW_MQ=260041.00;ReadPosRankSum=0.600;SOR=0.608	GT:AD:DP:GQ:PL	0/1:39,32:71:99:1032,0,1354
+20	10039371	.	T	G	1345.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.260e+00;ClippingRankSum=0.00;DP=74;ExcessHet=3.0103;FS=6.144;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=18.18;RAW_MQ=266400.00;ReadPosRankSum=0.510;SOR=1.031	GT:AD:DP:GQ:PL	0/1:34,40:74:99:1353,0,1194
+20	10040772	.	C	CT	2019.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.69;PG=0;QD=28.84;RAW_MQ=211048.00;SOR=0.811	GT:AD:DP:GQ:PL	1/1:0,70:70:99:2033,210,0
+20	10040812	.	AT	A	2631.03	.	AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;PG=0;QD=36.76;RAW_MQ=203299.00;SOR=0.721	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2645,214,0
+20	10040821	.	T	A	1192.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.100e-02;ClippingRankSum=0.00;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.60;MQRankSum=-9.700e-02;PG=0;QD=15.29;RAW_MQ=199699.00;ReadPosRankSum=-1.410e+00;SOR=0.688	GT:AD:DP:GQ:PL	0/1:38,40:78:99:1200,0,1099
+20	10041304	.	C	T	2780.06	.	AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.40;PG=3;QD=30.54;RAW_MQ=247010.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,68:68:99:2794,204,0
+20	10041701	.	A	ATATG	1433.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;ClippingRankSum=0.00;DP=78;ExcessHet=3.0103;FS=3.477;MLEAC=1;MLEAF=0.500;MQ=58.90;MQRankSum=0.340;PG=0;QD=25.60;RAW_MQ=270590.00;ReadPosRankSum=0.328;SOR=0.260	GT:AD:DP:GQ:PL	0/1:8,48:56:58:1441,0,58
+20	10042319	.	C	T	2673.06	.	AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;PG=10;QD=21.53;RAW_MQ=229851.00;SOR=1.033	GT:AD:DP:GQ:PL	1/1:0,66:66:99:2687,199,0
+20	10042761	.	A	G	3568.06	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=0;QD=34.87;RAW_MQ=327600.00;SOR=1.389	GT:AD:DP:GQ:PL	1/1:0,91:91:99:3582,272,0
+20	10042829	.	A	G	3070.06	.	AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;PG=11;QD=31.04;RAW_MQ=278569.00;SOR=0.855	GT:AD:DP:GQ:PL	1/1:0,78:78:99:3084,235,0
+20	10043002	.	A	T	1308.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.99;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=15.22;RAW_MQ=313200.00;ReadPosRankSum=0.178;SOR=0.434	GT:AD:DP:GQ:PL	0/1:48,38:86:99:1316,0,1659
+20	10044849	.	A	G	2106.06	.	AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;PG=0;QD=27.86;RAW_MQ=213241.00;SOR=1.316	GT:AD:DP:GQ:PL	1/1:0,59:59:99:2120,177,0
+20	10045078	.	G	T	3286.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;PG=2;QD=34.17;RAW_MQ=279389.00;SOR=0.876	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3300,244,0
+20	10045642	.	G	C	3122.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;PG=0;QD=28.60;RAW_MQ=286610.00;SOR=0.821	GT:AD:DP:GQ:PL	1/1:0,81:81:99:3136,243,0
+20	10046178	.	AAGAAAGAAAG	A	2183.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.22;PG=15;QD=25.57;RAW_MQ=144145.00;SOR=0.859	GT:AD:DP:GQ:PL	1/1:0,50:50:99:2197,152,0
+20	10046537	.	A	G	840.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.909e+00;ClippingRankSum=0.00;DP=57;ExcessHet=3.0103;FS=3.724;MLEAC=1;MLEAF=0.500;MQ=54.50;MQRankSum=0.395;PG=9;QD=14.75;RAW_MQ=169333.00;ReadPosRankSum=0.412;SOR=1.262	GT:AD:DP:GQ:PL	0/1:28,29:57:99:848,0,902
+20	10050828	.	T	C	1248.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.704e+00;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=2.887;MLEAC=1;MLEAF=0.500;MQ=59.74;MQRankSum=0.892;PG=1;QD=14.52;RAW_MQ=310441.00;ReadPosRankSum=0.073;SOR=0.521	GT:AD:DP:GQ:PL	0/1:49,37:86:99:1256,0,1768
+20	10051448	.	T	C	1155.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.010e-01;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=3.687;MLEAC=1;MLEAF=0.500;MQ=59.08;MQRankSum=-1.404e+00;PG=1;QD=16.51;RAW_MQ=247851.00;ReadPosRankSum=-5.490e-01;SOR=0.302	GT:AD:DP:GQ:PL	0/1:35,35:70:99:1163,0,1150
+20	10052688	.	C	A	1083.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=3.135;MLEAC=1;MLEAF=0.500;MQ=59.76;MQRankSum=0.870;PG=0;QD=14.07;RAW_MQ=274969.00;ReadPosRankSum=1.56;SOR=0.379	GT:AD:DP:GQ:PL	0/1:45,32:77:99:1091,0,1645
+20	10058022	.	T	C	996.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.346e+00;ClippingRankSum=0.00;DP=68;ExcessHet=3.0103;FS=0.920;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=0.466;PG=0;QD=14.66;RAW_MQ=237579.00;ReadPosRankSum=-4.530e-01;SOR=0.849	GT:AD:DP:GQ:PL	0/1:36,32:68:99:1004,0,1261
+20	10062935	.	C	CA	122.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.34;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.23;MQRankSum=-1.405e+00;PG=0;QD=8.17;RAW_MQ=232368.00;ReadPosRankSum=-4.930e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:5,10:23:99:130,0,101
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+20	10067090	.	C	A	2019.06	.	AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;PG=4;QD=30.20;RAW_MQ=166789.00;SOR=0.729	GT:AD:DP:GQ:PL	1/1:0,55:55:99:2033,164,0
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+20	10067722	.	A	C	2161.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=4;QD=31.67;RAW_MQ=198000.00;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
+20	10068158	.	GTGTATATATATA	G	96.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.520e-01;ClippingRankSum=0.00;DP=29;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=0.328;PG=0;QD=13.80;RAW_MQ=93364.00;ReadPosRankSum=-2.530e-01;SOR=0.061	GT:AD:DP:GQ:PGT:PID:PL	0/1:3,4:7:57:0|1:10068158_GTGTATATATATA_G:104,0,57
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+20	10070602	.	T	C	2706.06	.	AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.74;PG=0;QD=32.63;RAW_MQ=255364.00;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
+20	10070936	.	T	A	3646.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;PG=0;QD=30.36;RAW_MQ=279633.00;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,81:81:99:1|1:10070936_T_A:3660,247,0
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+20	10074240	.	T	C	3421.06	.	AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;PG=13;QD=35.18;RAW_MQ=307369.00;SOR=0.922	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3435,255,0
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+20	10075168	.	C	T	3627.06	.	AC=2;AF=1.00;AN=2;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;PG=0;QD=32.49;RAW_MQ=309981.00;SOR=0.997	GT:AD:DP:GQ:PL	1/1:0,88:88:99:3641,264,0
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+20	10088699	.	C	T	797.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.80;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=16.952;MLEAC=1;MLEAF=0.500;MQ=56.31;MQRankSum=-3.140e+00;PG=10;QD=12.87;RAW_MQ=199738.00;ReadPosRankSum=-5.770e-01;SOR=1.914	GT:AD:DP:GQ:PL	0/1:36,26:62:99:805,0,1088
+20	10088730	.	G	A	993.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.224;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=15.383;MLEAC=1;MLEAF=0.500;MQ=53.06;MQRankSum=-4.839e+00;PG=10;QD=19.11;RAW_MQ=149199.00;ReadPosRankSum=0.433;SOR=1.592	GT:AD:DP:GQ:PGT:PID:PL	0/1:29,23:52:99:0|1:10088730_G_A:1001,0,1152
+20	10088736	.	A	C	1102.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;ClippingRankSum=0.00;DP=56;ExcessHet=3.0103;FS=9.673;MLEAC=1;MLEAF=0.500;MQ=51.85;MQRankSum=-5.169e+00;PG=10;QD=20.05;RAW_MQ=150523.00;ReadPosRankSum=-4.200e-02;SOR=0.851	GT:AD:DP:GQ:PGT:PID:PL	0/1:28,27:55:99:0|1:10088730_G_A:1110,0,1194
+20	10088747	.	A	G	1132.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877e+00;ClippingRankSum=0.00;DP=56;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.25;MQRankSum=-4.907e+00;PG=9;QD=20.97;RAW_MQ=147080.00;ReadPosRankSum=-3.390e-01;SOR=1.092	GT:AD:DP:GQ:PGT:PID:PL	0/1:25,29:54:99:0|1:10088730_G_A:1140,0,995
+20	10088799	.	G	A	1039.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.50;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=52.86;MQRankSum=-2.498e+00;PG=11;QD=19.62;RAW_MQ=150881.00;ReadPosRankSum=1.35;SOR=1.003	GT:AD:DP:GQ:PL	0/1:22,31:53:99:1047,0,617
+20	10088895	.	C	T	553.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.46;ClippingRankSum=0.00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.76;MQRankSum=0.577;PG=8;QD=13.50;RAW_MQ=135291.00;ReadPosRankSum=0.907;SOR=0.653	GT:AD:DP:GQ:PL	0/1:23,18:41:99:561,0,673
+20	10088968	.	C	CAAA	1205.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.497;ClippingRankSum=0.00;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750e+00;PG=5;QD=22.75;RAW_MQ=177808.00;ReadPosRankSum=1.02;SOR=1.012	GT:AD:DP:GQ:PGT:PID:PL	0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367
+20	10088980	.	T	C	1268.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585e+00;ClippingRankSum=0.00;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232e+00;PG=10;QD=18.66;RAW_MQ=176353.00;ReadPosRankSum=0.999;SOR=0.709	GT:AD:DP:GQ:PGT:PID:PL	0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627
+20	10088985	.	T	C	1199.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920e-01;ClippingRankSum=0.00;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248e+00;PG=10;QD=16.21;RAW_MQ=191764.00;ReadPosRankSum=1.38;SOR=0.742	GT:AD:DP:GQ:PGT:PID:PL	0/1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729
+20	10089441	.	A	G	1200.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-9.480e-01;PG=0;QD=15.80;RAW_MQ=270841.00;ReadPosRankSum=0.161;SOR=1.363	GT:AD:DP:GQ:PL	0/1:37,39:76:99:1208,0,1313
+20	10089525	.	C	T	1569.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.86;ClippingRankSum=0.00;DP=82;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=1.53;PG=10;QD=19.38;RAW_MQ=290210.00;ReadPosRankSum=0.428;SOR=0.617	GT:AD:DP:GQ:PL	0/1:38,43:81:99:1577,0,1088
+20	10090289	.	CA	C	414.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.39;PG=5;QD=12.19;RAW_MQ=287682.00;ReadPosRankSum=-2.230e-01;SOR=0.859	GT:AD:DP:GQ:PL	0/1:14,20:38:99:422,0,230
+20	10090764	.	A	G	861.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659e+00;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=16;QD=13.68;RAW_MQ=226800.00;ReadPosRankSum=0.695;SOR=0.310	GT:AD:DP:GQ:PL	0/1:34,29:63:99:869,0,1207
+20	10090970	.	T	C	1278.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.840e-01;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.47;MQRankSum=1.51;PG=0;QD=18.53;RAW_MQ=247538.00;ReadPosRankSum=0.429;SOR=0.518	GT:AD:DP:GQ:PL	0/1:33,36:69:99:1286,0,1092
+20	10091214	.	C	T	1270.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;ClippingRankSum=0.00;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-9.160e-01;PG=0;QD=18.15;RAW_MQ=249769.00;ReadPosRankSum=0.392;SOR=0.625	GT:AD:DP:GQ:PL	0/1:33,37:70:99:1278,0,1110
+20	10092415	.	A	G	1656.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731e+00;ClippingRankSum=0.00;DP=102;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=16.40;RAW_MQ=367200.00;ReadPosRankSum=-7.000e-02;SOR=0.665	GT:AD:DP:GQ:PL	0/1:52,49:101:99:1664,0,1902
+20	10092927	.	G	T	127.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.507e+00;ClippingRankSum=0.00;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-3.009e+00;PG=0;QD=1.77;RAW_MQ=257282.00;ReadPosRankSum=-4.416e+00;SOR=5.279	GT:AD:DP:GQ:PL	0/1:59,13:72:99:135,0,1864
+20	10093568	.	GT	G	356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.426;ClippingRankSum=0.00;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=0.410;PG=3;QD=10.49;RAW_MQ=203561.00;ReadPosRankSum=0.987;SOR=0.751	GT:AD:DP:GQ:PL	0/1:17,17:42:99:364,0,386
+20	10093923	.	T	A	1096.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.670e-01;ClippingRankSum=0.00;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=0.358;PG=0;QD=16.37;RAW_MQ=234704.00;ReadPosRankSum=-2.256e+00;SOR=0.772	GT:AD:DP:GQ:PL	0/1:35,32:67:99:1104,0,1257
+20	10094251	.	T	A	1291.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;ClippingRankSum=0.00;DP=63;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;PG=0;QD=20.83;RAW_MQ=226800.00;ReadPosRankSum=1.73;SOR=1.211	GT:AD:DP:GQ:PL	0/1:26,36:62:99:1299,0,781
+20	10094582	.	A	G	944.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388e+00;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=1.27;PG=0;QD=13.69;RAW_MQ=254210.00;ReadPosRankSum=-5.270e-01;SOR=0.772	GT:AD:DP:GQ:PL	0/1:39,30:69:99:952,0,1350
+20	10094774	.	C	T	1057.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.840e-01;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=0.962;PG=0;QD=14.10;RAW_MQ=274441.00;ReadPosRankSum=0.494;SOR=0.690	GT:AD:DP:GQ:PL	0/1:40,35:75:99:1065,0,1282
+20	10095432	.	GTGATGATGA	G	869.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.27;ClippingRankSum=0.00;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431e+00;PG=6;QD=17.39;RAW_MQ=227748.00;ReadPosRankSum=0.660;SOR=0.460	GT:AD:DP:GQ:PL	0/1:27,23:50:99:877,0,2108
+20	10095741	.	A	G	1096.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.340e-01;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.39;MQRankSum=-2.313e+00;PG=0;QD=15.67;RAW_MQ=237128.00;ReadPosRankSum=-3.260e-01;SOR=0.515	GT:AD:DP:GQ:PL	0/1:36,34:70:99:1104,0,1233
+20	10096293	.	C	T	1376.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.66;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQRankSum=1.40;PG=0;QD=18.36;RAW_MQ=260861.00;ReadPosRankSum=0.012;SOR=0.638	GT:AD:DP:GQ:PL	0/1:37,38:75:99:1384,0,1258
+20	10096596	.	C	T	1583.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.612;PG=0;QD=18.20;RAW_MQ=300461.00;ReadPosRankSum=0.166;SOR=0.640	GT:AD:DP:GQ:PL	0/1:40,47:87:99:1591,0,1273
+20	10096768	.	A	C	1703.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.764e+00;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=3.983;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=-1.609e+00;PG=12;QD=18.72;RAW_MQ=319323.00;ReadPosRankSum=0.541;SOR=0.445	GT:AD:DP:GQ:PL	0/1:42,49:91:99:1711,0,1452
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+20	10096905	.	TA	T	1630.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.550e-01;ClippingRankSum=0.00;DP=83;ExcessHet=3.0103;FS=11.159;MLEAC=1;MLEAF=0.500;MQ=59.27;MQRankSum=-1.677e+00;PG=13;QD=19.65;RAW_MQ=291579.00;ReadPosRankSum=0.397;SOR=1.775	GT:AD:DP:GQ:PGT:PID:PL	0/1:40,43:83:99:0|1:10096899_G_T:1638,0,1623
+20	10096933	.	G	C	1532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914e+00;ClippingRankSum=0.00;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.802e+00;PG=13;QD=18.03;RAW_MQ=298779.00;ReadPosRankSum=0.238;SOR=1.534	GT:AD:DP:GQ:PGT:PID:PL	0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770
+20	10096958	.	G	A	1787.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.84;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-1.701e+00;PG=15;QD=19.43;RAW_MQ=323979.00;ReadPosRankSum=-1.860e+00;SOR=1.387	GT:AD:DP:GQ:PGT:PID:PL	0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629
+20	10097075	.	T	G	1466.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533e+00;ClippingRankSum=0.00;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.389e+00;PG=12;QD=15.94;RAW_MQ=315628.00;ReadPosRankSum=-2.850e-01;SOR=0.628	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482
+20	10097101	.	C	CTTT	1121.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134e+00;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=5.060;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-2.428e+00;PG=5;QD=18.69;RAW_MQ=252294.00;ReadPosRankSum=1.11;SOR=0.277	GT:AD:DP:GQ:PL	0/1:34,26:64:99:1129,0,1306
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+20	10097626	.	C	A	647.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.09;ClippingRankSum=0.00;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-1.331e+00;PG=0;QD=13.49;RAW_MQ=162820.00;ReadPosRankSum=1.15;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957
+20	10097789	.	T	C	709.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157e+00;ClippingRankSum=0.00;DP=61;ExcessHet=3.0103;FS=5.374;MLEAC=1;MLEAF=0.500;MQ=57.89;MQRankSum=-2.805e+00;PG=13;QD=12.45;RAW_MQ=204439.00;ReadPosRankSum=-9.200e-02;SOR=0.756	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190
+20	10097928	.	G	A	591.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203e+00;ClippingRankSum=0.00;DP=40;ExcessHet=3.0103;FS=1.315;MLEAC=1;MLEAF=0.500;MQ=58.25;MQRankSum=-1.654e+00;PG=13;QD=16.43;RAW_MQ=135723.00;ReadPosRankSum=0.057;SOR=0.951	GT:AD:DP:GQ:PL	0/1:17,19:36:99:599,0,586
+20	10098110	.	G	C	607.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=58.71;MQRankSum=-1.477e+00;PG=13;QD=16.88;RAW_MQ=124082.00;ReadPosRankSum=-7.140e-01;SOR=0.069	GT:AD:DP:GQ:PGT:PID:PL	0/1:19,17:36:99:0|1:10098110_G_C:615,0,727
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+20	10098237	.	A	T	265.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.000e-03;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.40;MQRankSum=-1.742e+00;PG=1;QD=20.43;RAW_MQ=37064.00;ReadPosRankSum=0.277;SOR=0.836	GT:AD:DP:GQ:PGT:PID:PL	0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273
+20	10098265	.	T	C	154.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;ClippingRankSum=0.00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQRankSum=-1.834e+00;PG=0;QD=25.77;RAW_MQ=10564.00;ReadPosRankSum=0.00;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59
+20	10098885	.	C	CA	463.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.165;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.89;MQRankSum=-4.449e+00;PG=11;QD=14.95;RAW_MQ=77157.00;ReadPosRankSum=-1.590e-01;SOR=0.518	GT:AD:DP:GQ:PL	0/1:17,14:31:99:471,0,572
+20	10098945	.	T	C	473.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=3.882;MLEAC=1;MLEAF=0.500;MQ=51.15;MQRankSum=-2.504e+00;PG=11;QD=21.53;RAW_MQ=57553.00;ReadPosRankSum=0.837;SOR=2.368	GT:AD:DP:GQ:PL	0/1:9,13:22:99:481,0,248
+20	10098987	.	C	T	400.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.13;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=7.005;MLEAC=1;MLEAF=0.500;MQ=51.88;MQRankSum=-2.734e+00;PG=0;QD=16.69;RAW_MQ=64586.00;ReadPosRankSum=0.348;SOR=2.925	GT:AD:DP:GQ:PL	0/1:11,13:24:99:408,0,350
+20	10099029	.	T	C	355.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.809e+00;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=2.032;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641e+00;PG=13;QD=12.70;RAW_MQ=79617.00;ReadPosRankSum=-7.930e-01;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
+20	10099034	.	C	A	355.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.76;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=4.265;MLEAC=1;MLEAF=0.500;MQ=53.32;MQRankSum=-3.641e+00;PG=13;QD=12.70;RAW_MQ=79617.00;ReadPosRankSum=-1.540e+00;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,10:28:99:0|1:10099029_T_C:363,0,768
+20	10099044	.	A	C	355.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148e+00;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418e+00;PG=13;QD=14.82;RAW_MQ=59851.00;ReadPosRankSum=-2.625e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:363,0,768
+20	10099046	.	T	C	325.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.165e+00;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQRankSum=-4.418e+00;PG=13;QD=13.57;RAW_MQ=59851.00;ReadPosRankSum=-2.686e+00;SOR=0.515	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,9:24:99:0|1:10099029_T_C:333,0,603
+20	10099055	.	T	C	277.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554e+00;ClippingRankSum=0.00;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.46;MQRankSum=-4.316e+00;PG=13;QD=12.07;RAW_MQ=58555.00;ReadPosRankSum=-2.131e+00;SOR=0.665	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,8:23:99:0|1:10099029_T_C:285,0,673
+20	10099079	.	C	T	137.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=0.00;DP=29;ExcessHet=3.0103;FS=1.862;MLEAC=1;MLEAF=0.500;MQ=52.09;MQRankSum=-2.821e+00;PG=13;QD=4.75;RAW_MQ=78698.00;ReadPosRankSum=1.97;SOR=1.289	GT:AD:DP:GQ:PGT:PID:PL	0/1:23,6:29:99:0|1:10099029_T_C:145,0,886
+20	10099111	.	T	TTTTGTTTG	686.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.207e+00;ClippingRankSum=0.00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.12;MQRankSum=-4.071e+00;PG=7;QD=19.62;RAW_MQ=109737.00;ReadPosRankSum=-1.200e-01;SOR=0.511	GT:AD:DP:GQ:PL	0/1:22,13:35:99:694,0,802
+20	10099140	.	G	T	1026.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140e-01;ClippingRankSum=0.00;DP=62;ExcessHet=3.0103;FS=2.241;MLEAC=1;MLEAF=0.500;MQ=55.72;MQRankSum=-2.469e+00;PG=12;QD=16.56;RAW_MQ=192512.00;ReadPosRankSum=0.169;SOR=1.114	GT:AD:DP:GQ:PL	0/1:30,32:62:99:1034,0,931
+20	10099190	.	G	T	1055.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-02;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQRankSum=-1.711e+00;PG=11;QD=16.24;RAW_MQ=220251.00;ReadPosRankSum=-1.418e+00;SOR=0.776	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1063,0,1154
+20	10099220	.	A	G	598.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.664e+00;ClippingRankSum=0.00;DP=45;ExcessHet=3.0103;FS=1.137;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-2.596e+00;PG=14;QD=13.30;RAW_MQ=149477.00;ReadPosRankSum=0.331;SOR=0.519	GT:AD:DP:GQ:PL	0/1:25,20:45:99:606,0,873
+20	10099250	.	G	A	720.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.17;ClippingRankSum=0.00;DP=37;ExcessHet=3.0103;FS=7.195;MLEAC=1;MLEAF=0.500;MQ=56.71;MQRankSum=-2.272e+00;PG=0;QD=19.48;RAW_MQ=119006.00;ReadPosRankSum=0.169;SOR=0.162	GT:AD:DP:GQ:PL	0/1:16,21:37:99:728,0,424
+20	10099535	.	G	A	1356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=5.03;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=2.172;MLEAC=1;MLEAF=0.500;MQ=59.00;MQRankSum=-1.418e+00;PG=13;QD=20.87;RAW_MQ=226251.00;ReadPosRankSum=-5.080e-01;SOR=0.408	GT:AD:DP:GQ:PL	0/1:26,39:65:99:1364,0,686
+20	10099565	.	C	T	1367.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.60;ClippingRankSum=0.00;DP=69;ExcessHet=3.0103;FS=8.736;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=-1.266e+00;PG=13;QD=19.82;RAW_MQ=243410.00;ReadPosRankSum=0.740;SOR=0.191	GT:AD:DP:GQ:PL	0/1:31,38:69:99:1375,0,994
+20	10099755	.	C	T	1119.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.55;ClippingRankSum=0.00;DP=66;ExcessHet=3.0103;FS=2.074;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-2.200e-02;PG=13;QD=17.23;RAW_MQ=232610.00;ReadPosRankSum=-6.840e-01;SOR=0.446	GT:AD:DP:GQ:PL	0/1:33,32:65:99:1127,0,1148
+20	10099832	.	A	G	1094.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.563e+00;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=4.632;MLEAC=1;MLEAF=0.500;MQ=58.96;MQRankSum=0.869;PG=16;QD=15.20;RAW_MQ=250276.00;ReadPosRankSum=0.213;SOR=0.871	GT:AD:DP:GQ:PL	0/1:39,33:72:99:1102,0,1430
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf
index 7aea75f525d..c14b9b2bf4a 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-75-gcfe332a,Date="Thu Mar 17 14:29:20 EDT 2016",Epoch=1458239360191,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1422/GTEX-RVPV-0003/v1/GTEX-RVPV-0003.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[20:10000000-11000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[DepthPerSampleHC, StrandBiasBySample, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf --include-non-variant-sites true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combine.single.sample.pipeline.1.vcf --intervals 20:10,030,000-10,033,000 --intervals 20:10,386,000-10,386,500 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:38 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -120,7 +119,6 @@
 ##contig=<ID=NC_007605,length=171823,assembly=b37>
 ##contig=<ID=hs37d5,length=35477943,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37_decoy.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GTEX-RVPV-0003
 20	10030000	.	T	.	.	.	DP=21	GT:DP:RGQ	0/0:21:63
 20	10030001	.	T	.	.	.	DP=21	GT:DP:RGQ	0/0:21:63
@@ -310,7 +308,7 @@
 20	10030185	.	C	.	.	.	DP=21	GT:DP:RGQ	0/0:21:63
 20	10030186	.	A	.	.	.	DP=21	GT:DP:RGQ	0/0:21:63
 20	10030187	.	C	.	.	.	DP=21	GT:DP:RGQ	0/0:21:63
-20	10030188	.	T	A	898.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.481e+00;ClippingRankSum=0.00;DP=86;ExcessHet=3.0103;FS=1.794;MLEAC=1;MLEAF=0.500;MQ=57.95;MQRankSum=1.49;QD=10.45;RAW_MQ=288777.00;ReadPosRankSum=0.334;SOR=0.495	GT:AD:DP:GQ:PL	0/1:46,40:86:99:906,0,1192
+20	10030188	.	T	A	898.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.481e+00;ClippingRankSum=0.00;DP=86;ExcessHet=3.0103;FS=1.794;MLEAC=1;MLEAF=0.500;MQ=57.95;MQRankSum=1.49;QD=10.45;RAW_MQ=288777.00;ReadPosRankSum=0.334;SOR=0.495	GT:AD:DP:GQ:PL	0/1:46,40:86:99:906,0,1192
 20	10030189	.	G	.	.	.	DP=23	GT:DP:RGQ	0/0:23:63
 20	10030190	.	T	.	.	.	DP=23	GT:DP:RGQ	0/0:23:63
 20	10030191	.	G	.	.	.	DP=23	GT:DP:RGQ	0/0:23:63
@@ -574,7 +572,7 @@
 20	10030449	.	A	.	.	.	DP=20	GT:DP:RGQ	0/0:20:45
 20	10030450	.	T	.	.	.	DP=20	GT:DP:RGQ	0/0:20:45
 20	10030451	.	G	.	.	.	DP=20	GT:DP:RGQ	0/0:20:45
-20	10030452	.	G	A	349.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.840e+00;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=8.929;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=1.52;QD=18.40;RAW_MQ=61179.00;ReadPosRankSum=0.854;SOR=0.045	GT:AD:DP:GQ:PL	0/1:6,13:19:99:357,0,170
+20	10030452	.	G	A	349.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.840e+00;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=8.929;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=1.52;QD=18.40;RAW_MQ=61179.00;ReadPosRankSum=0.854;SOR=0.045	GT:AD:DP:GQ:PL	0/1:6,13:19:99:357,0,170
 20	10030453	.	A	.	.	.	DP=16	GT:DP:RGQ	0/0:16:32
 20	10030454	.	C	.	.	.	DP=16	GT:DP:RGQ	0/0:16:32
 20	10030455	.	C	.	.	.	DP=16	GT:DP:RGQ	0/0:16:32
@@ -1053,7 +1051,7 @@
 20	10030928	.	G	.	.	.	DP=2	GT:DP:RGQ	0/0:2:6
 20	10030929	.	A	.	.	.	DP=2	GT:DP:RGQ	0/0:2:6
 20	10030930	.	C	.	.	.	DP=2	GT:DP:RGQ	0/0:2:6
-20	10030931	.	C	A	67.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.64;RAW_MQ=7200.00;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
+20	10030931	.	C	A	67.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.66;RAW_MQ=7200.00;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
 20	10030932	.	G	.	.	.	DP=2	GT:DP:RGQ	0/0:2:6
 20	10030933	.	A	.	.	.	DP=2	GT:DP:RGQ	0/0:2:6
 20	10030934	.	A	.	.	.	DP=2	GT:DP:RGQ	0/0:2:6
@@ -2535,7 +2533,7 @@
 20	10032410	.	A	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
 20	10032411	.	G	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
 20	10032412	.	C	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
-20	10032413	.	T	G	476.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;ClippingRankSum=0.00;DP=32;ExcessHet=3.0103;FS=3.254;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-8.190e-01;QD=14.89;RAW_MQ=112969.00;ReadPosRankSum=0.099;SOR=1.493	GT:AD:DP:GQ:PL	0/1:14,18:32:99:484,0,333
+20	10032413	.	T	G	476.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;ClippingRankSum=0.00;DP=32;ExcessHet=3.0103;FS=3.254;MLEAC=1;MLEAF=0.500;MQ=59.42;MQRankSum=-8.190e-01;QD=14.89;RAW_MQ=112969.00;ReadPosRankSum=0.099;SOR=1.493	GT:AD:DP:GQ:PL	0/1:14,18:32:99:484,0,333
 20	10032414	.	T	.	.	.	DP=26	GT:DP:RGQ	0/0:26:60
 20	10032415	.	T	.	.	.	DP=26	GT:DP:RGQ	0/0:26:60
 20	10032416	.	A	.	.	.	DP=26	GT:DP:RGQ	0/0:26:60
@@ -3136,7 +3134,7 @@
 20	10386010	.	G	.	.	.	DP=24	GT:DP:RGQ	0/0:24:60
 20	10386011	.	A	.	.	.	DP=24	GT:DP:RGQ	0/0:24:60
 20	10386012	.	G	.	.	.	DP=24	GT:DP:RGQ	0/0:24:60
-20	10386013	.	C	A	584.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.050e-01;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=5.155;MLEAC=1;MLEAF=0.500;MQ=57.93;MQRankSum=0.695;QD=9.13;RAW_MQ=214783.00;ReadPosRankSum=0.650;SOR=1.382	GT:AD:DP:GQ:PL	0/1:38,26:64:99:592,0,982
+20	10386013	.	C	A	584.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.050e-01;ClippingRankSum=0.00;DP=64;ExcessHet=3.0103;FS=5.155;MLEAC=1;MLEAF=0.500;MQ=57.93;MQRankSum=0.695;QD=9.13;RAW_MQ=214783.00;ReadPosRankSum=0.650;SOR=1.382	GT:AD:DP:GQ:PL	0/1:38,26:64:99:592,0,982
 20	10386014	.	C	.	.	.	DP=65	GT:DP:RGQ	0/0:65:99
 20	10386015	.	C	.	.	.	DP=65	GT:DP:RGQ	0/0:65:99
 20	10386016	.	A	.	.	.	DP=65	GT:DP:RGQ	0/0:65:99
@@ -3182,7 +3180,7 @@
 20	10386056	.	G	.	.	.	DP=65	GT:DP:RGQ	0/0:65:99
 20	10386057	.	A	.	.	.	DP=65	GT:DP:RGQ	0/0:65:99
 20	10386058	.	C	.	.	.	DP=65	GT:DP:RGQ	0/0:65:99
-20	10386059	.	G	A	1026.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.188;ClippingRankSum=0.00;DP=100;ExcessHet=3.0103;FS=1.625;MLEAC=1;MLEAF=0.500;MQ=58.30;MQRankSum=1.21;QD=10.37;RAW_MQ=339921.00;ReadPosRankSum=-3.340e-01;SOR=0.769	GT:AD:DP:GQ:PL	0/1:54,45:99:99:1034,0,1274
+20	10386059	.	G	A	1026.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.188;ClippingRankSum=0.00;DP=100;ExcessHet=3.0103;FS=1.625;MLEAC=1;MLEAF=0.500;MQ=58.30;MQRankSum=1.21;QD=10.37;RAW_MQ=339921.00;ReadPosRankSum=-3.340e-01;SOR=0.769	GT:AD:DP:GQ:PL	0/1:54,45:99:99:1034,0,1274
 20	10386060	.	T	.	.	.	DP=34	GT:DP:RGQ	0/0:34:63
 20	10386061	.	G	.	.	.	DP=34	GT:DP:RGQ	0/0:34:63
 20	10386062	.	T	.	.	.	DP=34	GT:DP:RGQ	0/0:34:63
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.2.include_nonvariant.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.2.include_nonvariant.vcf
index 4a51ecadd0b..3ccb3508ca9 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.2.include_nonvariant.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.2.include_nonvariant.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-75-gcfe332a,Date="Thu Mar 17 14:29:39 EDT 2016",Epoch=1458239379116,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1422/GTEX-QXCU-0004/v1/GTEX-QXCU-0004.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[20:10000000-11000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[DepthPerSampleHC, StrandBiasBySample, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.2.include_nonvariant.vcf --include-non-variant-sites true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combine.single.sample.pipeline.2.vcf --intervals 20:10,030,000-10,033,000 --intervals 20:10,386,000-10,386,500 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:38 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -120,7 +119,6 @@
 ##contig=<ID=NC_007605,length=171823,assembly=b37>
 ##contig=<ID=hs37d5,length=35477943,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37_decoy.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GTEX-QXCU-0004
 20	10030000	.	T	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
 20	10030001	.	T	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
@@ -310,7 +308,7 @@
 20	10030185	.	C	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
 20	10030186	.	A	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
 20	10030187	.	C	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
-20	10030188	.	T	A	516.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.102e+00;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=2.357;MLEAC=1;MLEAF=0.500;MQ=58.84;MQRankSum=-1.604e+00;QD=9.75;RAW_MQ=186963.00;ReadPosRankSum=1.28;SOR=1.069	GT:AD:DP:GQ:PL	0/1:30,23:53:99:524,0,874
+20	10030188	.	T	A	516.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.102e+00;ClippingRankSum=0.00;DP=54;ExcessHet=3.0103;FS=2.357;MLEAC=1;MLEAF=0.500;MQ=58.84;MQRankSum=-1.604e+00;QD=9.75;RAW_MQ=186963.00;ReadPosRankSum=1.28;SOR=1.069	GT:AD:DP:GQ:PL	0/1:30,23:53:99:524,0,874
 20	10030189	.	G	.	.	.	DP=25	GT:DP:RGQ	0/0:25:63
 20	10030190	.	T	.	.	.	DP=25	GT:DP:RGQ	0/0:25:63
 20	10030191	.	G	.	.	.	DP=25	GT:DP:RGQ	0/0:25:63
@@ -574,7 +572,7 @@
 20	10030449	.	A	.	.	.	DP=25	GT:DP:RGQ	0/0:25:63
 20	10030450	.	T	.	.	.	DP=25	GT:DP:RGQ	0/0:25:63
 20	10030451	.	G	.	.	.	DP=25	GT:DP:RGQ	0/0:25:36
-20	10030452	.	G	A	148.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123e+00;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=7.140;MLEAC=1;MLEAF=0.500;MQ=59.15;MQRankSum=-1.366e+00;QD=6.75;RAW_MQ=76969.00;ReadPosRankSum=0.924;SOR=2.368	GT:AD:DP:GQ:PL	0/1:15,7:22:99:156,0,434
+20	10030452	.	G	A	148.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123e+00;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=7.140;MLEAC=1;MLEAF=0.500;MQ=59.15;MQRankSum=-1.366e+00;QD=6.76;RAW_MQ=76969.00;ReadPosRankSum=0.924;SOR=2.368	GT:AD:DP:GQ:PL	0/1:15,7:22:99:156,0,434
 20	10030453	.	A	.	.	.	DP=24	GT:DP:RGQ	0/0:24:66
 20	10030454	.	C	.	.	.	DP=24	GT:DP:RGQ	0/0:24:66
 20	10030455	.	C	.	.	.	DP=24	GT:DP:RGQ	0/0:24:66
@@ -2535,7 +2533,7 @@
 20	10032410	.	A	.	.	.	DP=23	GT:DP:RGQ	0/0:23:63
 20	10032411	.	G	.	.	.	DP=23	GT:DP:RGQ	0/0:23:63
 20	10032412	.	C	.	.	.	DP=23	GT:DP:RGQ	0/0:23:63
-20	10032413	.	T	G	602.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.020;ClippingRankSum=0.00;DP=33;ExcessHet=3.0103;FS=1.574;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=0.00;QD=18.83;RAW_MQ=116569.00;ReadPosRankSum=2.55;SOR=1.162	GT:AD:DP:GQ:PL	0/1:12,20:32:99:610,0,369
+20	10032413	.	T	G	602.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.020;ClippingRankSum=0.00;DP=33;ExcessHet=3.0103;FS=1.574;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=0.00;QD=18.83;RAW_MQ=116569.00;ReadPosRankSum=2.55;SOR=1.162	GT:AD:DP:GQ:PL	0/1:12,20:32:99:610,0,369
 20	10032414	.	T	.	.	.	DP=26	GT:DP:RGQ	0/0:26:60
 20	10032415	.	T	.	.	.	DP=26	GT:DP:RGQ	0/0:26:60
 20	10032416	.	A	.	.	.	DP=26	GT:DP:RGQ	0/0:26:60
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf
index 9bcb63f94ed..4735c5f3b96 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-75-gcfe332a,Date="Thu Mar 17 14:30:02 EDT 2016",Epoch=1458239402264,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1422/GTEX-OXRP-0003/v1/GTEX-OXRP-0003.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[20:10000000-11000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[DepthPerSampleHC, StrandBiasBySample, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf --include-non-variant-sites true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combine.single.sample.pipeline.3.vcf --intervals 20:10,030,000-10,033,000 --intervals 20:10,386,000-10,386,500 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:39 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -120,7 +119,6 @@
 ##contig=<ID=NC_007605,length=171823,assembly=b37>
 ##contig=<ID=hs37d5,length=35477943,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37_decoy.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GTEX-OXRP-0003
 20	10030000	.	T	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
 20	10030001	.	T	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
@@ -310,7 +308,7 @@
 20	10030185	.	C	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
 20	10030186	.	A	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
 20	10030187	.	C	.	.	.	DP=21	GT:DP:RGQ	0/0:21:60
-20	10030188	.	T	A	319.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.520e-01;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=1.383;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.88;RAW_MQ=129600.00;ReadPosRankSum=-7.530e-01;SOR=1.009	GT:AD:DP:GQ:PL	0/1:22,14:36:99:327,0,587
+20	10030188	.	T	A	319.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.520e-01;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=1.383;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.88;RAW_MQ=129600.00;ReadPosRankSum=-7.530e-01;SOR=1.009	GT:AD:DP:GQ:PL	0/1:22,14:36:99:327,0,587
 20	10030189	.	G	.	.	.	DP=25	GT:DP:RGQ	0/0:25:60
 20	10030190	.	T	.	.	.	DP=25	GT:DP:RGQ	0/0:25:60
 20	10030191	.	G	.	.	.	DP=25	GT:DP:RGQ	0/0:25:60
@@ -574,7 +572,7 @@
 20	10030449	.	A	.	.	.	DP=18	GT:DP:RGQ	0/0:18:36
 20	10030450	.	T	.	.	.	DP=18	GT:DP:RGQ	0/0:18:36
 20	10030451	.	G	.	.	.	DP=18	GT:DP:RGQ	0/0:18:36
-20	10030452	.	G	A	193.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282e+00;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=1.871;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.19;RAW_MQ=68400.00;ReadPosRankSum=0.694;SOR=1.402	GT:AD:DP:GQ:PL	0/1:10,9:19:99:201,0,259
+20	10030452	.	G	A	193.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282e+00;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=1.871;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.19;RAW_MQ=68400.00;ReadPosRankSum=0.694;SOR=1.402	GT:AD:DP:GQ:PL	0/1:10,9:19:99:201,0,259
 20	10030453	.	A	.	.	.	DP=13	GT:DP:RGQ	0/0:13:36
 20	10030454	.	C	.	.	.	DP=13	GT:DP:RGQ	0/0:13:36
 20	10030455	.	C	.	.	.	DP=13	GT:DP:RGQ	0/0:13:36
@@ -1920,7 +1918,7 @@
 20	10031795	.	G	.	.	.	DP=2	GT:DP:RGQ	./.:2:0
 20	10031796	.	T	.	.	.	DP=2	GT:DP:RGQ	./.:2:0
 20	10031797	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:2:0
-20	10031798	.	G	A	37.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.00;QD=18.64;RAW_MQ=2738.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
+20	10031798	.	G	A	37.32	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.00;QD=18.66;RAW_MQ=2738.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
 20	10031799	.	T	.	.	.	.	GT:DP:RGQ	./.:0:0
 20	10031800	.	T	.	.	.	.	GT:DP:RGQ	./.:0:0
 20	10031801	.	A	.	.	.	.	GT:DP:RGQ	./.:0:0
@@ -2535,7 +2533,7 @@
 20	10032410	.	A	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
 20	10032411	.	G	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
 20	10032412	.	C	.	.	.	DP=22	GT:DP:RGQ	0/0:22:63
-20	10032413	.	T	G	546.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.805;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=1.220;MLEAC=1;MLEAF=0.500;MQ=58.49;MQRankSum=0.650;QD=10.31;RAW_MQ=181348.00;ReadPosRankSum=0.422;SOR=0.994	GT:AD:DP:GQ:PL	0/1:31,22:53:99:554,0,845
+20	10032413	.	T	G	546.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.805;ClippingRankSum=0.00;DP=53;ExcessHet=3.0103;FS=1.220;MLEAC=1;MLEAF=0.500;MQ=58.49;MQRankSum=0.650;QD=10.31;RAW_MQ=181348.00;ReadPosRankSum=0.422;SOR=0.994	GT:AD:DP:GQ:PL	0/1:31,22:53:99:554,0,845
 20	10032414	.	T	.	.	.	DP=32	GT:DP:RGQ	0/0:32:63
 20	10032415	.	T	.	.	.	DP=32	GT:DP:RGQ	0/0:32:63
 20	10032416	.	A	.	.	.	DP=32	GT:DP:RGQ	0/0:32:63
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf
index d83b1bc2dbb..d472ccdbdaa 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-75-gcfe332a,Date="Thu Mar 17 14:29:20 EDT 2016",Epoch=1458239360191,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1422/GTEX-RVPV-0003/v1/GTEX-RVPV-0003.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[20:10000000-11000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[DepthPerSampleHC, StrandBiasBySample, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf --include-non-variant-sites true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined.single.sample.pipeline.gatk3.vcf --intervals 20:10,030,000-10,033,000 --intervals 20:10,386,000-10,386,500 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:39 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -36,7 +35,6 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/cnorman/projects/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GTEX-OXRP-0003	GTEX-QXCU-0004	GTEX-RVPV-0003
 20	10030000	.	T	.	.	.	DP=64	GT:DP:RGQ	0/0:21:60	0/0:22:63	0/0:21:63
 20	10030001	.	T	.	.	.	DP=64	GT:DP:RGQ	0/0:21:60	0/0:22:63	0/0:21:63
@@ -226,7 +224,7 @@
 20	10030185	.	C	.	.	.	DP=64	GT:DP:RGQ	0/0:21:60	0/0:22:63	0/0:21:63
 20	10030186	.	A	.	.	.	DP=64	GT:DP:RGQ	0/0:21:60	0/0:22:63	0/0:21:63
 20	10030187	.	C	.	.	.	DP=64	GT:DP:RGQ	0/0:21:60	0/0:22:63	0/0:21:63
-20	10030188	.	T	A	1746.93	.	AC=3;AF=0.500;AN=6;BaseQRankSum=-1.481e+00;ClippingRankSum=0.00;DP=176;ExcessHet=6.9897;FS=0.000;MLEAC=3;MLEAF=0.500;MQ=58.65;MQRankSum=0.00;QD=9.98;RAW_MQ=605340.00;ReadPosRankSum=0.334;SOR=0.737	GT:AD:DP:GQ:PL	0/1:22,14:36:99:327,0,587	0/1:30,23:53:99:524,0,874	0/1:46,40:86:99:906,0,1192
+20	10030188	.	T	A	1746.97	.	AC=3;AF=0.500;AN=6;BaseQRankSum=-1.481e+00;ClippingRankSum=0.00;DP=176;ExcessHet=6.9897;FS=0.000;MLEAC=3;MLEAF=0.500;MQ=58.65;MQRankSum=0.00;QD=9.98;RAW_MQ=605340.00;ReadPosRankSum=0.334;SOR=0.737	GT:AD:DP:GQ:PL	0/1:22,14:36:99:327,0,587	0/1:30,23:53:99:524,0,874	0/1:46,40:86:99:906,0,1192
 20	10030189	.	G	.	.	.	DP=73	GT:DP:RGQ	0/0:25:60	0/0:25:63	0/0:23:63
 20	10030190	.	T	.	.	.	DP=73	GT:DP:RGQ	0/0:25:60	0/0:25:63	0/0:23:63
 20	10030191	.	G	.	.	.	DP=73	GT:DP:RGQ	0/0:25:60	0/0:25:63	0/0:23:63
@@ -490,7 +488,7 @@
 20	10030449	.	A	.	.	.	DP=63	GT:DP:RGQ	0/0:18:36	0/0:25:63	0/0:20:45
 20	10030450	.	T	.	.	.	DP=63	GT:DP:RGQ	0/0:18:36	0/0:25:63	0/0:20:45
 20	10030451	.	G	.	.	.	DP=63	GT:DP:RGQ	0/0:18:36	0/0:25:36	0/0:20:45
-20	10030452	.	G	A	703.93	.	AC=3;AF=0.500;AN=6;BaseQRankSum=-1.282e+00;ClippingRankSum=0.00;DP=60;ExcessHet=6.9897;FS=2.252;MLEAC=3;MLEAF=0.500;MQ=58.67;MQRankSum=0.00;QD=11.73;RAW_MQ=206548.00;ReadPosRankSum=0.854;SOR=1.052	GT:AD:DP:GQ:PL	0/1:10,9:19:99:201,0,259	0/1:15,7:22:99:156,0,434	0/1:6,13:19:99:357,0,170
+20	10030452	.	G	A	703.97	.	AC=3;AF=0.500;AN=6;BaseQRankSum=-1.282e+00;ClippingRankSum=0.00;DP=60;ExcessHet=6.9897;FS=2.252;MLEAC=3;MLEAF=0.500;MQ=58.67;MQRankSum=0.00;QD=11.73;RAW_MQ=206548.00;ReadPosRankSum=0.854;SOR=1.052	GT:AD:DP:GQ:PL	0/1:10,9:19:99:201,0,259	0/1:15,7:22:99:156,0,434	0/1:6,13:19:99:357,0,170
 20	10030453	.	A	.	.	.	DP=53	GT:DP:RGQ	0/0:13:36	0/0:24:66	0/0:16:32
 20	10030454	.	C	.	.	.	DP=53	GT:DP:RGQ	0/0:13:36	0/0:24:66	0/0:16:32
 20	10030455	.	C	.	.	.	DP=53	GT:DP:RGQ	0/0:13:36	0/0:24:66	0/0:16:32
@@ -969,7 +967,7 @@
 20	10030928	.	G	.	.	.	DP=2	GT:DP:RGQ	./.:0:0	./.:0:0	0/0:2:6
 20	10030929	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:0:0	./.:0:0	0/0:2:6
 20	10030930	.	C	.	.	.	DP=2	GT:DP:RGQ	./.:0:0	./.:0:0	0/0:2:6
-20	10030931	.	C	A	69.18	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.59;RAW_MQ=7200.00;SOR=2.303	GT:AD:DP:GQ:PL	./.:0,0:0:.:0,0,0	./.:0,0:0:.:0,0,0	1/1:0,2:2:6:79,6,0
+20	10030931	.	C	A	69.24	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.62;RAW_MQ=7200.00;SOR=2.303	GT:AD:DP:GQ:PL	./.:0,0:0:.:0,0,0	./.:0,0:0:.:0,0,0	1/1:0,2:2:6:79,6,0
 20	10030932	.	G	.	.	.	DP=2	GT:DP:RGQ	./.:0:0	./.:0:0	0/0:2:6
 20	10030933	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:0:0	./.:0:0	0/0:2:6
 20	10030934	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:0:0	./.:0:0	0/0:2:6
@@ -1836,7 +1834,7 @@
 20	10031795	.	G	.	.	.	DP=2	GT:DP:RGQ	./.:2:0	./.:0:0	./.:0:0
 20	10031796	.	T	.	.	.	DP=2	GT:DP:RGQ	./.:2:0	./.:0:0	./.:0:0
 20	10031797	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:2:0	./.:0:0	./.:0:0
-20	10031798	.	G	A	39.18	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.00;QD=19.59;RAW_MQ=2738.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0	./.:0,0:0:.:0,0,0	./.:0,0:0:.:0,0,0
+20	10031798	.	G	A	39.24	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.00;QD=19.62;RAW_MQ=2738.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0	./.:0,0:0:.:0,0,0	./.:0,0:0:.:0,0,0
 20	10031799	.	T	.	.	.	.	GT:DP:RGQ	./.:0:0	./.:0:0	./.:0:0
 20	10031800	.	T	.	.	.	.	GT:DP:RGQ	./.:0:0	./.:0:0	./.:0:0
 20	10031801	.	A	.	.	.	.	GT:DP:RGQ	./.:0:0	./.:0:0	./.:0:0
@@ -2451,7 +2449,7 @@
 20	10032410	.	A	.	.	.	DP=66	GT:DP:RGQ	0/0:22:63	0/0:23:63	0/0:21:60
 20	10032411	.	G	.	.	.	DP=66	GT:DP:RGQ	0/0:22:63	0/0:23:63	0/0:21:60
 20	10032412	.	C	.	.	.	DP=66	GT:DP:RGQ	0/0:22:63	0/0:23:63	0/0:21:60
-20	10032413	.	T	G	1637.93	.	AC=3;AF=0.500;AN=6;BaseQRankSum=0.387;ClippingRankSum=0.00;DP=118;ExcessHet=6.9897;FS=3.735;MLEAC=3;MLEAF=0.500;MQ=59.01;MQRankSum=0.00;QD=14.00;RAW_MQ=410886.00;ReadPosRankSum=0.422;SOR=1.144	GT:AD:DP:GQ:PL	0/1:31,22:53:99:554,0,845	0/1:12,20:32:99:610,0,369	0/1:14,18:32:99:484,0,333
+20	10032413	.	T	G	1637.97	.	AC=3;AF=0.500;AN=6;BaseQRankSum=0.387;ClippingRankSum=0.00;DP=118;ExcessHet=6.9897;FS=3.735;MLEAC=3;MLEAF=0.500;MQ=59.01;MQRankSum=0.00;QD=14.00;RAW_MQ=410886.00;ReadPosRankSum=0.422;SOR=1.144	GT:AD:DP:GQ:PL	0/1:31,22:53:99:554,0,845	0/1:12,20:32:99:610,0,369	0/1:14,18:32:99:484,0,333
 20	10032414	.	T	.	.	.	DP=84	GT:DP:RGQ	0/0:32:63	0/0:26:60	0/0:26:60
 20	10032415	.	T	.	.	.	DP=84	GT:DP:RGQ	0/0:32:63	0/0:26:60	0/0:26:60
 20	10032416	.	A	.	.	.	DP=84	GT:DP:RGQ	0/0:32:63	0/0:26:60	0/0:26:60
@@ -3052,7 +3050,7 @@
 20	10386010	.	G	.	.	.	DP=65	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:24:60
 20	10386011	.	A	.	.	.	DP=65	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:24:60
 20	10386012	.	G	.	.	.	DP=65	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:24:60
-20	10386013	.	C	A	583.25	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-5.050e-01;ClippingRankSum=0.00;DP=105;ExcessHet=3.0103;FS=5.155;MLEAC=1;MLEAF=0.167;MQ=57.93;MQRankSum=0.695;QD=9.11;RAW_MQ=214783.00;ReadPosRankSum=0.650;SOR=1.382	GT:AD:DP:GQ:PL	0/0:21,0:21:60:0,60,686	0/0:20,0:20:60:0,60,611	0/1:38,26:64:99:592,0,982
+20	10386013	.	C	A	583.29	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-5.050e-01;ClippingRankSum=0.00;DP=105;ExcessHet=3.0103;FS=5.155;MLEAC=1;MLEAF=0.167;MQ=57.93;MQRankSum=0.695;QD=9.11;RAW_MQ=214783.00;ReadPosRankSum=0.650;SOR=1.382	GT:AD:DP:GQ:PL	0/0:21,0:21:60:0,60,686	0/0:20,0:20:60:0,60,611	0/1:38,26:64:99:592,0,982
 20	10386014	.	C	.	.	.	DP=106	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:65:99
 20	10386015	.	C	.	.	.	DP=106	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:65:99
 20	10386016	.	A	.	.	.	DP=106	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:65:99
@@ -3098,7 +3096,7 @@
 20	10386056	.	G	.	.	.	DP=106	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:65:99
 20	10386057	.	A	.	.	.	DP=106	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:65:99
 20	10386058	.	C	.	.	.	DP=106	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:65:99
-20	10386059	.	G	A	1025.25	.	AC=1;AF=0.167;AN=6;BaseQRankSum=0.188;ClippingRankSum=0.00;DP=141;ExcessHet=3.0103;FS=1.625;MLEAC=1;MLEAF=0.167;MQ=58.30;MQRankSum=1.21;QD=10.36;RAW_MQ=339921.00;ReadPosRankSum=-3.340e-01;SOR=0.769	GT:AD:DP:GQ:PL	0/0:21,0:21:60:0,60,686	0/0:20,0:20:60:0,60,611	0/1:54,45:99:99:1034,0,1274
+20	10386059	.	G	A	1025.29	.	AC=1;AF=0.167;AN=6;BaseQRankSum=0.188;ClippingRankSum=0.00;DP=141;ExcessHet=3.0103;FS=1.625;MLEAC=1;MLEAF=0.167;MQ=58.30;MQRankSum=1.21;QD=10.36;RAW_MQ=339921.00;ReadPosRankSum=-3.340e-01;SOR=0.769	GT:AD:DP:GQ:PL	0/0:21,0:21:60:0,60,686	0/0:20,0:20:60:0,60,611	0/1:54,45:99:99:1034,0,1274
 20	10386060	.	T	.	.	.	DP=75	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:34:63
 20	10386061	.	G	.	.	.	DP=75	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:34:63
 20	10386062	.	T	.	.	.	DP=75	GT:DP:RGQ	0/0:21:60	0/0:20:60	0/0:34:63
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/gvcf.basepairResolution.includeNonVariantSites.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/gvcf.basepairResolution.includeNonVariantSites.vcf
index f6e94c415f9..8bfad45af05 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/gvcf.basepairResolution.includeNonVariantSites.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/gvcf.basepairResolution.includeNonVariantSites.vcf
@@ -8,7 +8,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/56/l8cj86792b773xql3374k3dcmtd1k5/T/genotypegvcf8453174056672361677.vcf --include-non-variant-sites true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --allow-old-rms-mapping-quality-annotation-data true  --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="January 21, 2020 1:52:13 PM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -113,7 +112,6 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 20	10000000	.	T	.	.	.	DP=52	GT:AD:DP:RGQ	0/0:52:52:99
 20	10000001	.	T	.	.	.	DP=54	GT:AD:DP:RGQ	0/0:54:54:99
@@ -4885,16 +4883,16 @@
 20	10004767	.	A	.	.	.	DP=43	GT:AD:DP:RGQ	0/0:43:43:75
 20	10004768	.	C	.	.	.	DP=43	GT:AD:DP:RGQ	0/0:43:43:72
 20	10004769	.	TAAAACTATGC	T	675.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.710e-01;ClippingRankSum=-5.370e-01;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.95;MQ0=0;MQRankSum=-4.022e+00;QD=15.35;ReadPosRankSum=0.585;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
-20	10004770	.	A	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004771	.	A	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004772	.	A	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004773	.	A	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004774	.	C	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004775	.	T	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004776	.	A	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004777	.	T	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004778	.	G	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
-20	10004779	.	C	.	Infinity	.	DP=48;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:44:99
+20	10004770	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004771	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004772	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004773	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004774	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004775	.	T	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004776	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004777	.	T	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004778	.	G	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
+20	10004779	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
 20	10004780	.	A	.	.	.	DP=47	GT:AD:DP:RGQ	./.:31:47:0
 20	10004781	.	A	.	.	.	DP=47	GT:AD:DP:RGQ	0/0:47:47:99
 20	10004782	.	A	.	.	.	DP=47	GT:AD:DP:RGQ	0/0:47:47:99
@@ -6935,6 +6933,10 @@
 20	10006817	.	A	.	.	.	DP=38	GT:AD:DP:RGQ	0/0:37:38:12
 20	10006818	.	A	.	.	.	DP=37	GT:AD:DP:RGQ	0/0:36:37:12
 20	10006819	.	AAAAC	A	1513.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.67;MQ0=0;QD=29.11;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
+20	10006820	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
+20	10006821	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
+20	10006822	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
+20	10006823	.	C	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
 20	10006824	.	A	.	.	.	DP=40	GT:AD:DP:RGQ	./.:8:40:0
 20	10006825	.	A	.	.	.	DP=42	GT:AD:DP:RGQ	0/0:42:42:99
 20	10006826	.	A	.	.	.	DP=42	GT:AD:DP:RGQ	0/0:42:42:99
@@ -8258,6 +8260,7 @@
 20	10008144	.	A	.	.	.	DP=50	GT:AD:DP:RGQ	./.:50:50:0
 20	10008145	.	T	.	.	.	DP=51	GT:AD:DP:RGQ	./.:51:51:0
 20	10008146	.	TA	T	1727.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.35;MQ0=0;QD=28.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1741,142,0
+20	10008147	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1741,142,0
 20	10008148	.	A	.	.	.	DP=49	GT:AD:DP:RGQ	./.:1:49:0
 20	10008149	.	A	.	.	.	DP=49	GT:AD:DP:RGQ	0/0:49:49:99
 20	10008150	.	A	.	.	.	DP=49	GT:AD:DP:RGQ	0/0:49:49:99
@@ -9059,20 +9062,21 @@
 20	10008946	.	T	.	.	.	DP=24	GT:AD:DP:RGQ	0/0:23:24:15
 20	10008947	.	T	.	.	.	DP=24	GT:AD:DP:RGQ	0/0:24:24:12
 20	10008948	.	TA	T	1057.03	.	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=168.45;MQ0=0;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
+20	10008949	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
 20	10008950	.	A	.	.	.	DP=24	GT:AD:DP:RGQ	./.:5:24:0
 20	10008951	.	A	.	.	.	DP=24	GT:AD:DP:RGQ	./.:15:24:0
 20	10008952	.	CACACACACACA	C,CCACACACACA	988.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
-20	10008953	.	A	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008954	.	C	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008955	.	A	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008956	.	C	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008957	.	A	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008958	.	C	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008959	.	A	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008960	.	C	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008961	.	A	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008962	.	C	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
-20	10008963	.	A	.	Infinity	.	DP=25;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:21:99
+20	10008953	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008954	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008955	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008956	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008957	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008958	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008959	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008960	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008961	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008962	.	C	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
+20	10008963	.	A	*	0	LowQual	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
 20	10008964	.	C	.	.	.	DP=23	GT:AD:DP:RGQ	0/0:23:23:60
 20	10008965	.	A	.	.	.	DP=23	GT:AD:DP:RGQ	0/0:23:23:60
 20	10008966	.	C	.	.	.	DP=23	GT:AD:DP:RGQ	0/0:23:23:60
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf
index 8d0b86978a5..cb6a7144157 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-75-gcfe332a,Date="Thu Mar 17 14:29:20 EDT 2016",Epoch=1458239360191,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1422/GTEX-RVPV-0003/v1/GTEX-RVPV-0003.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[20:10000000-11000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[DepthPerSampleHC, StrandBiasBySample, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf --include-non-variant-sites true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined.single.sample.pipeline.gatk3.vcf --intervals 20:10,012,730-10,012,740 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:39 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -36,7 +35,6 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/cnorman/projects/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GTEX-OXRP-0003	GTEX-QXCU-0004	GTEX-RVPV-0003
 20	10012730	.	G	.	.	.	DP=4	GT:DP:RGQ	0/0:2:6	./.:0:0	0/0:2:6
 20	10012731	.	C	.	.	.	DP=4	GT:DP:RGQ	0/0:2:6	./.:0:0	0/0:2:6
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf
index 0b8bfe251e6..13b3ea11481 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-75-gcfe332a,Date="Thu Mar 17 14:29:20 EDT 2016",Epoch=1458239360191,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1422/GTEX-RVPV-0003/v1/GTEX-RVPV-0003.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[20:10000000-11000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[DepthPerSampleHC, StrandBiasBySample, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf5082734211502181066.vcf --include-non-variant-sites true --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/combined.single.sample.pipeline.gatk3.vcf --intervals 20:10,096,905-10,096,907 --intervals 20:10624924-10624926 --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="April 23, 2019 3:18:01 PM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -36,11 +35,10 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/cnorman/projects/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GTEX-OXRP-0003	GTEX-QXCU-0004	GTEX-RVPV-0003
 20	10096905	.	TA	T	80.18	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.36;RAW_MQ=7200.00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10096899_G_T:90,6,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0
-20	10096906	.	A	.	7.04	LowQual	DP=2;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:2:6	0/0:0:0	0/0:0:0
+20	10096906	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10096899_G_T:90,6,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0
 20	10096907	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:2:0	./.:0:0	./.:0:0
 20	10624924	.	TCA	T	169.53	.	AC=2;AF=0.333;AN=6;BaseQRankSum=0.103;ClippingRankSum=0.00;DP=56;ExcessHet=3.9794;FS=1.657;MLEAC=2;MLEAF=0.333;MQ=55.03;MQRankSum=0.754;QD=5.30;RAW_MQ=142331.00;ReadPosRankSum=120.50;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:11,4:15:71:.:.:71,0,257	0/0:9,0:9:0:.:.:0,0,231	0/1:11,6:17:99:0|1:10624924_TCA_T:107,0,318
-20	10624925	.	C	.	159.31	.	DP=64;MLEAC=.;MLEAF=.	GT:DP:RGQ	0/0:15:71	0/0:17:13	0/0:17:99
-20	10624926	.	A	T,*	207.76	.	AC=2,1;AF=0.333,0.167;AN=6;BaseQRankSum=9.00;ClippingRankSum=9.00;DP=59;ExcessHet=6.9897;FS=0.000;MLEAC=2,1;MLEAF=0.333,0.167;MQ=44.19;MQRankSum=114.97;QD=4.72;RAW_MQ=115213.00;ReadPosRankSum=115.78;SOR=0.529	GT:AD:DP:GQ:PGT:PID:PL	0/2:11,0,4:15:71:.:.:71,104,374,0,269,257	0/1:7,5,0:12:99:.:.:150,0,191,171,206,378	0/1:11,6,0:17:68:1|0:10624924_TCA_T:68,0,217,100,234,335
+20	10624925	.	C	*	0	LowQual	AC=2;AF=0.333;AN=6;DP=64;ExcessHet=3.9794;FS=1.657;MLEAC=2;MLEAF=0.333;QD=0.00;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:11,4:15:71:.:.:71,0,257	0/0:17,0:17:13:.:.:0,13,557	0/1:11,6:17:99:0|1:10624924_TCA_T:107,0,318
+20	10624926	.	A	T,*	207.80	.	AC=2,1;AF=0.333,0.167;AN=6;BaseQRankSum=9.00;ClippingRankSum=9.00;DP=59;ExcessHet=6.9897;FS=0.000;MLEAC=2,1;MLEAF=0.333,0.167;MQ=44.19;MQRankSum=114.97;QD=4.72;RAW_MQ=115213.00;ReadPosRankSum=115.78;SOR=0.529	GT:AD:DP:GQ:PGT:PID:PL	0/2:11,0,4:15:71:.:.:71,104,374,0,269,257	0/1:7,5,0:12:99:.:.:150,0,191,171,206,378	0/1:11,6,0:17:68:1|0:10624924_TCA_T:68,0,217,100,234,335
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf
index dd2a2bd11a5..f7b0c121260 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf
@@ -8,7 +8,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:13 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -113,78 +112,77 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	.	C	T	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.110e-01;DP=38;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.172e+00;QD=16.67;ReadPosRankSum=-2.350e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
-20	10000211	.	C	T	659.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;ClippingRankSum=-1.927e+00;DP=42;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.89;MQ0=0;MQRankSum=-1.750e+00;QD=15.70;ReadPosRankSum=1.55;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
-20	10000439	.	T	G	1757.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.41;MQ0=0;QD=31.38;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
-20	10000598	.	T	A	1774.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.55;MQ0=0;QD=33.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
-20	10000694	.	G	A	982.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-9.000e-03;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.482;QD=18.54;ReadPosRankSum=1.54;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
-20	10000758	.	T	A	1683.03	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;QD=33.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1697,149,0
-20	10001019	.	T	G	114.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;ClippingRankSum=-3.470e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.65;MQ0=0;MQRankSum=-9.250e-01;QD=4.41;ReadPosRankSum=0.00;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
-20	10001298	.	T	A	1424.03	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=171.56;MQ0=0;QD=34.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
-20	10001436	.	A	AAGGCT	1872.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
-20	10001474	.	C	T	1614.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
-20	10001617	.	C	A	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=-8.430e-01;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.345e+00;QD=16.67;ReadPosRankSum=-2.810e-01;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
-20	10001628	.	G	A	1387.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;QD=30.97;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
-20	10001661	.	T	C	1559.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.28;MQ0=0;QD=27.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1573,108,0
-20	10001670	.	T	G	1559.03	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.63;MQ0=0;QD=28.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,32:32:99:1573,108,0
-20	10002058	.	T	G	1722.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;QD=25.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
-20	10002099	.	C	T	614.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.583e+00;DP=50;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.61;MQ0=0;MQRankSum=-1.719e+00;QD=12.29;ReadPosRankSum=1.85;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
-20	10002138	.	C	G	2143.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.52;MQ0=0;QD=29.56;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2157,147,0
-20	10002142	.	G	C	2143.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.31;MQ0=0;QD=30.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2157,147,0
-20	10002458	.	G	GTT,GTTT	1170.10	.	AC=1,1;AF=0.500,0.500;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=186.78;MQ0=0;QD=28.17;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,8,7:15:99:1187,229,144,270,0,185
-20	10002470	.	C	T	1218.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=179.57;MQ0=0;QD=26.80;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,29:29:86:1232,86,0
-20	10002625	.	G	T	1339.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
-20	10003021	.	C	T	1393.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=214.87;MQ0=0;QD=34.83;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
-20	10003358	.	A	C	377.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.209;ClippingRankSum=0.095;DP=32;ExcessHet=3.0103;FS=3.270;MLEAC=1;MLEAF=0.500;MQ=224.98;MQ0=0;MQRankSum=-1.710e-01;QD=11.80;ReadPosRankSum=1.12;SOR=1.445	GT:AD:DP:GQ:PL	0/1:18,14:32:99:385,0,504
-20	10003651	.	T	C	1401.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;QD=26.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
-20	10003692	.	A	G	1602.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.51;MQ0=0;QD=34.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1616,141,0
-20	10003832	.	G	A	1874.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.45;MQ0=0;QD=34.07;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,55:55:99:1888,165,0
-20	10004094	.	A	C	943.03	.	AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=101.97;MQ0=0;QD=31.43;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:957,90,0
-20	10004147	.	A	G	559.03	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;QD=24.31;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,23:23:66:573,66,0
-20	10004193	.	G	T	294.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.124;ClippingRankSum=-2.060e-01;DP=20;ExcessHet=3.0103;FS=9.556;MLEAC=1;MLEAF=0.500;MQ=86.94;MQ0=0;MQRankSum=0.289;QD=15.51;ReadPosRankSum=-1.197e+00;SOR=3.442	GT:AD:DP:GQ:PL	0/1:8,11:19:99:302,0,223
-20	10004222	.	C	CA	312.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.460e-01;ClippingRankSum=1.08;DP=27;ExcessHet=3.0103;FS=14.428;MLEAC=1;MLEAF=0.500;MQ=143.03;MQ0=0;MQRankSum=-2.770e-01;QD=13.59;ReadPosRankSum=-3.390e-01;SOR=0.969	GT:AD:DP:GQ:PL	0/1:12,11:23:99:320,0,341
-20	10004223	.	A	AG	283.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.90;ClippingRankSum=-1.642e+00;DP=31;ExcessHet=3.0103;FS=14.989;MLEAC=1;MLEAF=0.500;MQ=152.05;MQ0=0;MQRankSum=0.264;QD=9.15;ReadPosRankSum=1.36;SOR=2.640	GT:AD:DP:GQ:PL	0/1:19,12:31:99:291,0,501
-20	10004351	.	C	G	1638.03	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.76;MQ0=0;QD=30.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1652,132,0
-20	10004389	.	T	G	1896.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.38;MQ0=0;QD=31.98;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1910,156,0
-20	10004610	.	A	C	1600.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.18;MQ0=0;QD=32.65;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1614,146,0
-20	10004725	.	A	G	602.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.44;ClippingRankSum=-5.850e-01;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.84;MQ0=0;MQRankSum=1.95;QD=12.82;ReadPosRankSum=0.649;SOR=0.784	GT:AD:DP:GQ:PL	0/1:24,23:47:99:610,0,600
+20	10000117	.	C	T	633.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.110e-01;DP=38;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.172e+00;QD=16.67;ReadPosRankSum=-2.350e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
+20	10000211	.	C	T	659.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;ClippingRankSum=-1.927e+00;DP=42;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.89;MQ0=0;MQRankSum=-1.750e+00;QD=15.71;ReadPosRankSum=1.55;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
+20	10000439	.	T	G	1757.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.41;MQ0=0;QD=31.38;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
+20	10000598	.	T	A	1774.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.55;MQ0=0;QD=33.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
+20	10000694	.	G	A	982.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-9.000e-03;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.482;QD=18.54;ReadPosRankSum=1.54;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
+20	10000758	.	T	A	1683.06	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;QD=33.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1697,149,0
+20	10001019	.	T	G	114.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;ClippingRankSum=-3.470e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.65;MQ0=0;MQRankSum=-9.250e-01;QD=4.41;ReadPosRankSum=0.00;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
+20	10001298	.	T	A	1424.06	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=171.56;MQ0=0;QD=34.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
+20	10001436	.	A	AAGGCT	1872.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
+20	10001474	.	C	T	1614.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
+20	10001617	.	C	A	633.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=-8.430e-01;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.345e+00;QD=16.67;ReadPosRankSum=-2.810e-01;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
+20	10001628	.	G	A	1387.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;QD=30.97;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
+20	10001661	.	T	C	1559.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.28;MQ0=0;QD=27.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1573,108,0
+20	10001670	.	T	G	1559.06	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.63;MQ0=0;QD=28.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,32:32:99:1573,108,0
+20	10002058	.	T	G	1722.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;QD=25.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
+20	10002099	.	C	T	614.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.583e+00;DP=50;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.61;MQ0=0;MQRankSum=-1.719e+00;QD=12.29;ReadPosRankSum=1.85;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
+20	10002138	.	C	G	2143.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.52;MQ0=0;QD=29.56;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2157,147,0
+20	10002142	.	G	C	2143.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.31;MQ0=0;QD=30.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2157,147,0
+20	10002458	.	G	GTT,GTTT	1170.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=186.78;MQ0=0;QD=28.17;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,8,7:15:99:1187,229,144,270,0,185
+20	10002470	.	C	T	1218.06	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=179.57;MQ0=0;QD=26.80;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,29:29:86:1232,86,0
+20	10002625	.	G	T	1339.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
+20	10003021	.	C	T	1393.06	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=214.87;MQ0=0;QD=34.83;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
+20	10003358	.	A	C	377.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.209;ClippingRankSum=0.095;DP=32;ExcessHet=3.0103;FS=3.270;MLEAC=1;MLEAF=0.500;MQ=224.98;MQ0=0;MQRankSum=-1.710e-01;QD=11.80;ReadPosRankSum=1.12;SOR=1.445	GT:AD:DP:GQ:PL	0/1:18,14:32:99:385,0,504
+20	10003651	.	T	C	1401.06	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;QD=26.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
+20	10003692	.	A	G	1602.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.51;MQ0=0;QD=34.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1616,141,0
+20	10003832	.	G	A	1874.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.45;MQ0=0;QD=34.07;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,55:55:99:1888,165,0
+20	10004094	.	A	C	943.06	.	AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=101.97;MQ0=0;QD=31.44;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:957,90,0
+20	10004147	.	A	G	559.06	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;QD=24.31;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,23:23:66:573,66,0
+20	10004193	.	G	T	294.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.124;ClippingRankSum=-2.060e-01;DP=20;ExcessHet=3.0103;FS=9.556;MLEAC=1;MLEAF=0.500;MQ=86.94;MQ0=0;MQRankSum=0.289;QD=15.51;ReadPosRankSum=-1.197e+00;SOR=3.442	GT:AD:DP:GQ:PL	0/1:8,11:19:99:302,0,223
+20	10004222	.	C	CA	312.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.460e-01;ClippingRankSum=1.08;DP=27;ExcessHet=3.0103;FS=14.428;MLEAC=1;MLEAF=0.500;MQ=143.03;MQ0=0;MQRankSum=-2.770e-01;QD=13.59;ReadPosRankSum=-3.390e-01;SOR=0.969	GT:AD:DP:GQ:PL	0/1:12,11:23:99:320,0,341
+20	10004223	.	A	AG	283.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.90;ClippingRankSum=-1.642e+00;DP=31;ExcessHet=3.0103;FS=14.989;MLEAC=1;MLEAF=0.500;MQ=152.05;MQ0=0;MQRankSum=0.264;QD=9.15;ReadPosRankSum=1.36;SOR=2.640	GT:AD:DP:GQ:PL	0/1:19,12:31:99:291,0,501
+20	10004351	.	C	G	1638.06	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.76;MQ0=0;QD=30.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1652,132,0
+20	10004389	.	T	G	1896.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.38;MQ0=0;QD=31.98;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1910,156,0
+20	10004610	.	A	C	1600.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.18;MQ0=0;QD=32.65;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1614,146,0
+20	10004725	.	A	G	602.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.44;ClippingRankSum=-5.850e-01;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.84;MQ0=0;MQRankSum=1.95;QD=12.82;ReadPosRankSum=0.649;SOR=0.784	GT:AD:DP:GQ:PL	0/1:24,23:47:99:610,0,600
 20	10004769	.	TAAAACTATGC	T	675.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.710e-01;ClippingRankSum=-5.370e-01;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.95;MQ0=0;MQRankSum=-4.022e+00;QD=15.35;ReadPosRankSum=0.585;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
-20	10004874	.	A	C	1701.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.94;MQ0=0;QD=34.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1715,150,0
-20	10004887	.	A	G	579.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.979;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=222.04;MQ0=0;MQRankSum=-3.733e+00;QD=12.33;ReadPosRankSum=1.02;SOR=0.813	GT:AD:DP:GQ:PL	0/1:27,20:47:99:587,0,796
-20	10005010	.	C	T	1376.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=225.36;MQ0=0;QD=27.51;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
-20	10005427	.	C	T	1839.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;QD=34.06;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
-20	10005499	.	A	G	1798.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.64;ClippingRankSum=-4.720e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.00;QD=32.69;ReadPosRankSum=1.91;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1812,116,0
-20	10005587	.	A	G	821.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;ClippingRankSum=-1.027e+00;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-1.724e+00;QD=15.50;ReadPosRankSum=0.348;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
-20	10005723	.	A	G	1461.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;QD=31.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
-20	10006291	.	G	A	456.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
-20	10006404	.	A	C	1438.03	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.10;MQ0=0;QD=31.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1452,135,0
-20	10006682	.	T	A	1005.03	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
+20	10004874	.	A	C	1701.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.94;MQ0=0;QD=34.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1715,150,0
+20	10004887	.	A	G	579.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.979;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=222.04;MQ0=0;MQRankSum=-3.733e+00;QD=12.33;ReadPosRankSum=1.02;SOR=0.813	GT:AD:DP:GQ:PL	0/1:27,20:47:99:587,0,796
+20	10005010	.	C	T	1376.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=225.36;MQ0=0;QD=27.51;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
+20	10005427	.	C	T	1839.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;QD=34.06;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
+20	10005499	.	A	G	1798.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.64;ClippingRankSum=-4.720e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.00;QD=32.69;ReadPosRankSum=1.91;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1812,116,0
+20	10005587	.	A	G	821.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;ClippingRankSum=-1.027e+00;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-1.724e+00;QD=15.50;ReadPosRankSum=0.348;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
+20	10005723	.	A	G	1461.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;QD=31.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
+20	10006291	.	G	A	456.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
+20	10006404	.	A	C	1438.06	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.10;MQ0=0;QD=31.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1452,135,0
+20	10006682	.	T	A	1005.06	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
 20	10006819	.	AAAAC	A	1513.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.67;MQ0=0;QD=29.11;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
-20	10007150	.	G	C	537.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
-20	10007175	.	C	T	271.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.940e-01;ClippingRankSum=-6.930e-01;DP=25;ExcessHet=3.0103;FS=3.544;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.305;QD=10.86;ReadPosRankSum=0.804;SOR=0.260	GT:AD:DP:GQ:PL	0/1:15,10:25:99:279,0,474
-20	10007352	.	C	T	1476.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
-20	10007531	.	A	G	1654.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
-20	10007980	.	A	C	1658.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.35;MQ0=0;QD=33.16;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
-20	10008029	.	T	TA	1505.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
+20	10007150	.	G	C	537.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
+20	10007175	.	C	T	271.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.940e-01;ClippingRankSum=-6.930e-01;DP=25;ExcessHet=3.0103;FS=3.544;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.305;QD=10.87;ReadPosRankSum=0.804;SOR=0.260	GT:AD:DP:GQ:PL	0/1:15,10:25:99:279,0,474
+20	10007352	.	C	T	1476.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
+20	10007531	.	A	G	1654.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
+20	10007980	.	A	C	1658.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.35;MQ0=0;QD=33.16;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
+20	10008029	.	T	TA	1505.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
 20	10008146	.	TA	T	1727.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.35;MQ0=0;QD=28.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1741,142,0
-20	10008221	.	T	C	1822.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
-20	10008458	.	T	G	1627.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
-20	10008742	.	G	T	218.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.16;ClippingRankSum=1.35;DP=19;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=106.06;MQ0=0;MQRankSum=0.694;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
-20	10008758	.	C	CA	491.06	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
-20	10008921	.	C	CA	356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
+20	10008221	.	T	C	1822.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
+20	10008458	.	T	G	1627.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
+20	10008742	.	G	T	218.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.16;ClippingRankSum=1.35;DP=19;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=106.06;MQ0=0;MQRankSum=0.694;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
+20	10008758	.	C	CA	491.03	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
+20	10008921	.	C	CA	356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
 20	10008948	.	TA	T	1057.03	.	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=168.45;MQ0=0;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
-20	10008952	.	CACACACACACA	C,CCACACACACA	988.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
-20	10009227	.	A	G	875.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
-20	10009246	.	A	G	2043.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
-20	10009400	.	T	A	1620.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
-20	10009512	.	C	G	1516.03	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
-20	10009719	.	A	G	1091.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
-20	10009795	.	A	G	1171.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
-20	10009842	.	G	GAA	383.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;QD=14.76;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
-20	10009844	.	G	A	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
-20	10009871	.	A	G	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10008952	.	CACACACACACA	C,CCACACACACA	988.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
+20	10009227	.	A	G	875.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
+20	10009246	.	A	G	2043.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
+20	10009400	.	T	A	1620.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
+20	10009512	.	C	G	1516.06	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
+20	10009719	.	A	G	1091.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
+20	10009795	.	A	G	1171.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
+20	10009842	.	G	GAA	383.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;QD=14.75;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
+20	10009844	.	G	A	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10009871	.	A	G	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
 20	10009875	.	A	G,AGGGAGG	1479.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=192.36;MQ0=0;QD=26.61;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,14,11:25:99:1496,567,1162,680,0,1286
-20	10009879	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
-20	10009883	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
+20	10009879	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
+20	10009883	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf
index d37da858a37..c3f6733c055 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf
@@ -1,5 +1,6 @@
 ##fileformat=VCFv4.2
 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -9,7 +10,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcfExample1.vcf --intervals 20 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:14 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -116,9 +116,8 @@
 ##contig=<ID=NC_007605,length=171823>
 ##contig=<ID=hs37d5,length=35477943>
 ##reference=file:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta
-##source=GenotypeGVCFs
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
-20	69511	.	A	G	2270.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.17;DP=82;ExcessHet=3.0103;FS=3.716;MLEAC=2;MLEAF=1.00;MQ=31.05;MQ0=0;MQRankSum=-8.660e-01;QD=28.38;ReadPosRankSum=1.69;SOR=0.771	GT:AD:DP:GQ:PL	1/1:1,79:80:99:2284,207,0
-20	69635	.	C	T	81.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.15;MQ0=0;MQRankSum=1.30;QD=11.66;ReadPosRankSum=1.75;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:89:89,0,119
+20	69511	.	A	G	2270.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.17;DP=82;ExcessHet=3.0103;FS=3.716;MLEAC=2;MLEAF=1.00;MQ=31.05;MQ0=0;MQRankSum=-8.660e-01;QD=28.38;ReadPosRankSum=1.69;SOR=0.771	GT:AD:DP:GQ:PL	1/1:1,79:80:99:2284,207,0
+20	69635	.	C	T	81.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.15;MQ0=0;MQRankSum=1.30;QD=11.66;ReadPosRankSum=1.75;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:89:89,0,119
 20	69772	.	TTATC	T	81.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.15;MQ0=0;MQRankSum=1.30;QD=11.66;ReadPosRankSum=1.75;SOR=0.495	GT:AD:DP:GQ:PL	0/1:4,3:7:89:89,0,119
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionExpected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionExpected.vcf
index 29dfb9cc9f4..ed3441a4f85 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionExpected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionExpected.vcf
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.2
 ##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -10,7 +11,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionExpected.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletion.g.vcf --intervals 20:69512-69513 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:13 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -114,7 +114,6 @@
 ##contig=<ID=NC_007605,length=171823>
 ##contig=<ID=hs37d5,length=35477943>
 ##reference=file:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1	NA2
 20	69511	.	ACAC	A	2268.44	.	AC=2;AF=0.500;AN=4;DP=162;ExcessHet=0.7918;FS=3.716;MLEAC=2;MLEAF=0.500;QD=28.36;SOR=0.771	GT:AD:DP:GQ:MIN_GQ:PL	1/1:1,79:80:99:.:2284,207,0	0/0:82,0:82:99:99:0,122,1802
-20	69513	.	A	G,*	2415.89	.	AC=2,2;AF=0.500,0.500;AN=4;DP=160;ExcessHet=3.0103;FS=7.469;MLEAC=2,2;MLEAF=0.500,0.500;QD=15.10;SOR=0.712	GT:AD:DP:GQ:PL	2/2:1,0,79:80:99:2284,2287,2316,207,237,0	1/1:1,79,0:80:99:2233,233,0,2244,234,2333
+20	69513	.	A	G,*	2218.93	.	AC=2,2;AF=0.500,0.500;AN=4;DP=160;ExcessHet=3.0103;FS=7.469;MLEAC=2,2;MLEAF=0.500,0.500;QD=13.87;SOR=0.712	GT:AD:DP:GQ:PL	2/2:1,0,79:80:99:2284,2287,2316,207,237,0	1/1:1,79,0:80:99:2233,233,0,2244,234,2333
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionRestrictToStartExpected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionRestrictToStartExpected.vcf
index 81078911a2b..ed38eac19dd 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionRestrictToStartExpected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionRestrictToStartExpected.vcf
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.2
 ##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -10,7 +11,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletionRestrictToStartExpected.vcf --only-output-calls-starting-in-intervals true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/leadingDeletion.g.vcf --intervals 20:69512-69513 --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:13 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -114,6 +114,5 @@
 ##contig=<ID=NC_007605,length=171823>
 ##contig=<ID=hs37d5,length=35477943>
 ##reference=file:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1	NA2
-20	69513	.	A	G,*	2415.89	.	AC=2,2;AF=0.500,0.500;AN=4;DP=160;ExcessHet=3.0103;FS=7.469;MLEAC=2,2;MLEAF=0.500,0.500;QD=15.10;SOR=0.712	GT:AD:DP:GQ:PL	2/2:1,0,79:80:99:2284,2287,2316,207,237,0	1/1:1,79,0:80:99:2233,233,0,2244,234,2333
+20	69513	.	A	G,*	2218.93	.	AC=2,2;AF=0.500,0.500;AN=4;DP=160;ExcessHet=3.0103;FS=7.469;MLEAC=2,2;MLEAF=0.500,0.500;QD=13.87;SOR=0.712	GT:AD:DP:GQ:PL	2/2:1,0,79:80:99:2284,2287,2316,207,237,0	1/1:1,79,0:80:99:2233,233,0,2244,234,2333
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf
index bcfcfeed0f5..e159f7f5f80 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf
@@ -8,7 +8,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf --max-alternate-alleles 1 --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:15 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -113,78 +112,77 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	.	C	T	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.110e-01;DP=38;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.172e+00;QD=16.67;ReadPosRankSum=-2.350e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
-20	10000211	.	C	T	659.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;ClippingRankSum=-1.927e+00;DP=42;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.89;MQ0=0;MQRankSum=-1.750e+00;QD=15.70;ReadPosRankSum=1.55;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
-20	10000439	.	T	G	1757.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.41;MQ0=0;QD=31.38;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
-20	10000598	.	T	A	1774.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.55;MQ0=0;QD=33.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
-20	10000694	.	G	A	982.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-9.000e-03;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.482;QD=18.54;ReadPosRankSum=1.54;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
-20	10000758	.	T	A	1683.03	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;QD=33.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1697,149,0
-20	10001019	.	T	G	114.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;ClippingRankSum=-3.470e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.65;MQ0=0;MQRankSum=-9.250e-01;QD=4.41;ReadPosRankSum=0.00;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
-20	10001298	.	T	A	1424.03	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=171.56;MQ0=0;QD=34.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
-20	10001436	.	A	AAGGCT	1872.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
-20	10001474	.	C	T	1614.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
-20	10001617	.	C	A	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=-8.430e-01;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.345e+00;QD=16.67;ReadPosRankSum=-2.810e-01;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
-20	10001628	.	G	A	1387.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;QD=30.97;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
-20	10001661	.	T	C	1559.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.28;MQ0=0;QD=27.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1573,108,0
-20	10001670	.	T	G	1559.03	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.63;MQ0=0;QD=28.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,32:32:99:1573,108,0
-20	10002058	.	T	G	1722.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;QD=25.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
-20	10002099	.	C	T	614.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.583e+00;DP=50;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.61;MQ0=0;MQRankSum=-1.719e+00;QD=12.29;ReadPosRankSum=1.85;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
-20	10002138	.	C	G	2143.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.52;MQ0=0;QD=29.56;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2157,147,0
-20	10002142	.	G	C	2143.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.31;MQ0=0;QD=30.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2157,147,0
-20	10002458	.	G	GTT	1029.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=186.78;MQ0=0;QD=28.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,8:15:85:1043,85,0
-20	10002470	.	C	T	1218.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=179.57;MQ0=0;QD=26.80;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,29:29:86:1232,86,0
-20	10002625	.	G	T	1339.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
-20	10003021	.	C	T	1393.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=214.87;MQ0=0;QD=34.83;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
-20	10003358	.	A	C	377.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.209;ClippingRankSum=0.095;DP=32;ExcessHet=3.0103;FS=3.270;MLEAC=1;MLEAF=0.500;MQ=224.98;MQ0=0;MQRankSum=-1.710e-01;QD=11.80;ReadPosRankSum=1.12;SOR=1.445	GT:AD:DP:GQ:PL	0/1:18,14:32:99:385,0,504
-20	10003651	.	T	C	1401.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;QD=26.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
-20	10003692	.	A	G	1602.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.51;MQ0=0;QD=34.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1616,141,0
-20	10003832	.	G	A	1874.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.45;MQ0=0;QD=34.07;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,55:55:99:1888,165,0
-20	10004094	.	A	C	943.03	.	AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=101.97;MQ0=0;QD=31.43;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:957,90,0
-20	10004147	.	A	G	559.03	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;QD=24.31;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,23:23:66:573,66,0
-20	10004193	.	G	T	294.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.124;ClippingRankSum=-2.060e-01;DP=20;ExcessHet=3.0103;FS=9.556;MLEAC=1;MLEAF=0.500;MQ=86.94;MQ0=0;MQRankSum=0.289;QD=15.51;ReadPosRankSum=-1.197e+00;SOR=3.442	GT:AD:DP:GQ:PL	0/1:8,11:19:99:302,0,223
-20	10004222	.	C	CA	312.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.460e-01;ClippingRankSum=1.08;DP=27;ExcessHet=3.0103;FS=14.428;MLEAC=1;MLEAF=0.500;MQ=143.03;MQ0=0;MQRankSum=-2.770e-01;QD=13.59;ReadPosRankSum=-3.390e-01;SOR=0.969	GT:AD:DP:GQ:PL	0/1:12,11:23:99:320,0,341
-20	10004223	.	A	AG	283.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.90;ClippingRankSum=-1.642e+00;DP=31;ExcessHet=3.0103;FS=14.989;MLEAC=1;MLEAF=0.500;MQ=152.05;MQ0=0;MQRankSum=0.264;QD=9.15;ReadPosRankSum=1.36;SOR=2.640	GT:AD:DP:GQ:PL	0/1:19,12:31:99:291,0,501
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 20	10004769	.	TAAAACTATGC	T	675.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.710e-01;ClippingRankSum=-5.370e-01;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.95;MQ0=0;MQRankSum=-4.022e+00;QD=15.35;ReadPosRankSum=0.585;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
-20	10004874	.	A	C	1701.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.94;MQ0=0;QD=34.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1715,150,0
-20	10004887	.	A	G	579.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.979;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=222.04;MQ0=0;MQRankSum=-3.733e+00;QD=12.33;ReadPosRankSum=1.02;SOR=0.813	GT:AD:DP:GQ:PL	0/1:27,20:47:99:587,0,796
-20	10005010	.	C	T	1376.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=225.36;MQ0=0;QD=27.51;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
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+20	10005010	.	C	T	1376.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=225.36;MQ0=0;QD=27.51;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
+20	10005427	.	C	T	1839.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;QD=34.06;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
+20	10005499	.	A	G	1798.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.64;ClippingRankSum=-4.720e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.00;QD=32.69;ReadPosRankSum=1.91;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1812,116,0
+20	10005587	.	A	G	821.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;ClippingRankSum=-1.027e+00;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-1.724e+00;QD=15.50;ReadPosRankSum=0.348;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
+20	10005723	.	A	G	1461.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;QD=31.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
+20	10006291	.	G	A	456.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
+20	10006404	.	A	C	1438.06	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.10;MQ0=0;QD=31.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1452,135,0
+20	10006682	.	T	A	1005.06	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
 20	10006819	.	AAAAC	A	1513.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.67;MQ0=0;QD=29.11;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
-20	10007150	.	G	C	537.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
-20	10007175	.	C	T	271.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.940e-01;ClippingRankSum=-6.930e-01;DP=25;ExcessHet=3.0103;FS=3.544;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.305;QD=10.86;ReadPosRankSum=0.804;SOR=0.260	GT:AD:DP:GQ:PL	0/1:15,10:25:99:279,0,474
-20	10007352	.	C	T	1476.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
-20	10007531	.	A	G	1654.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
-20	10007980	.	A	C	1658.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.35;MQ0=0;QD=33.16;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
-20	10008029	.	T	TA	1505.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
+20	10007150	.	G	C	537.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
+20	10007175	.	C	T	271.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.940e-01;ClippingRankSum=-6.930e-01;DP=25;ExcessHet=3.0103;FS=3.544;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.305;QD=10.87;ReadPosRankSum=0.804;SOR=0.260	GT:AD:DP:GQ:PL	0/1:15,10:25:99:279,0,474
+20	10007352	.	C	T	1476.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
+20	10007531	.	A	G	1654.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
+20	10007980	.	A	C	1658.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.35;MQ0=0;QD=33.16;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
+20	10008029	.	T	TA	1505.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
 20	10008146	.	TA	T	1727.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.35;MQ0=0;QD=28.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1741,142,0
-20	10008221	.	T	C	1822.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
-20	10008458	.	T	G	1627.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
-20	10008742	.	G	T	218.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.16;ClippingRankSum=1.35;DP=19;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=106.06;MQ0=0;MQRankSum=0.694;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
-20	10008758	.	C	CA	491.06	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
-20	10008921	.	C	CA	356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
+20	10008221	.	T	C	1822.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
+20	10008458	.	T	G	1627.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
+20	10008742	.	G	T	218.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.16;ClippingRankSum=1.35;DP=19;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=106.06;MQ0=0;MQRankSum=0.694;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
+20	10008758	.	C	CA	491.03	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
+20	10008921	.	C	CA	356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
 20	10008948	.	TA	T	1057.03	.	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=168.45;MQ0=0;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
 20	10008952	.	CACACACACACA	C	595.60	.	AC=1;AF=0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=170.70;MQ0=0;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,12:21:99:603,0,609
-20	10009227	.	A	G	875.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
-20	10009246	.	A	G	2043.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
-20	10009400	.	T	A	1620.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
-20	10009512	.	C	G	1516.03	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
-20	10009719	.	A	G	1091.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
-20	10009795	.	A	G	1171.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
-20	10009842	.	G	GAA	383.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;QD=14.76;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
-20	10009844	.	G	A	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
-20	10009871	.	A	G	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
-20	10009875	.	A	G	921.60	.	AC=1;AF=0.500;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=192.36;MQ0=0;QD=26.61;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,14:25:99:929,0,595
-20	10009879	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
-20	10009883	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
+20	10009227	.	A	G	875.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
+20	10009246	.	A	G	2043.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
+20	10009400	.	T	A	1620.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
+20	10009512	.	C	G	1516.06	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
+20	10009719	.	A	G	1091.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
+20	10009795	.	A	G	1171.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
+20	10009842	.	G	GAA	383.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;QD=14.75;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
+20	10009844	.	G	A	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10009871	.	A	G	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10009875	.	A	G	921.64	.	AC=1;AF=0.500;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=192.36;MQ0=0;QD=26.61;SOR=0.693	GT:AD:DP:GQ:PL	0/1:0,14:25:99:929,0,595
+20	10009879	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
+20	10009883	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf
index f0e2d33b224..f8d5ab239c9 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf
@@ -13,12 +13,12 @@
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.CombineGVCFs=<ID=CombineGVCFs,Version=3.6-106-g94d8a6a,Date="Wed Jan 04 15:23:24 EST 2017",Epoch=1483561404402,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1:899875-899992] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false annotation=[AS_MQMateRankSumTest, AS_InsertSizeRankSum] dbsnp=(RodBinding name= source=UNBOUND) variant=[(RodBindingCollection [(RodBinding name=variant source=/seq/tng/methodsdev/data/sample_vcf/C1592/Exome/Homo_sapiens_assembly19/05C44993.20161114_1407.vcf.gz), (RodBinding name=variant2 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C29912.20161114_1407.vcf.gz), (RodBinding name=variant3 source=/seq/tng/methodsdev/data/sample_vcf/C1468/Exome/Homo_sapiens_assembly19/04C31948.20161114_1407.vcf.gz), (RodBinding name=variant4 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C31737.20161114_1407.vcf.gz), (RodBinding name=variant5 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/05C48752.20161114_1406.vcf.gz), (RodBinding name=variant6 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C31739.20161114_1406.vcf.gz), (RodBinding name=variant7 source=/seq/tng/methodsdev/data/sample_vcf/C1592/Exome/Homo_sapiens_assembly19/04C31240.20161114_1407.vcf.gz), (RodBinding name=variant8 source=/seq/tng/methodsdev/data/sample_vcf/C1592/Exome/Homo_sapiens_assembly19/05C44992.20161114_1407.vcf.gz), (RodBinding name=variant9 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C29170.20161114_1406.vcf.gz), (RodBinding name=variant10 source=/seq/tng/methodsdev/data/sample_vcf/C1468/Exome/Homo_sapiens_assembly19/08C77441.20161114_1407.vcf.gz), (RodBinding name=variant11 source=/seq/tng/methodsdev/data/sample_vcf/C1468/Exome/Homo_sapiens_assembly19/08C77440.20161114_1407.vcf.gz), (RodBinding name=variant12 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C32077.20161114_1407.vcf.gz), (RodBinding name=variant13 source=/seq/tng/methodsdev/data/sample_vcf/C1592/Exome/Homo_sapiens_assembly19/05C46546.20161114_1407.vcf.gz), (RodBinding name=variant14 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C29913.20161114_1406.vcf.gz), (RodBinding name=variant15 source=/seq/tng/methodsdev/data/sample_vcf/C1592/Exome/Homo_sapiens_assembly19/04C31241.20161114_1407.vcf.gz), (RodBinding name=variant16 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C29155.20161114_1407.vcf.gz), (RodBinding name=variant17 source=/seq/tng/methodsdev/data/sample_vcf/C1963/Exome/Homo_sapiens_assembly19/CHMI_CHMI3_Nex1.20161111_1044.vcf.gz), (RodBinding name=variant18 source=/seq/tng/methodsdev/data/sample_vcf/C1592/Exome/Homo_sapiens_assembly19/05C46545.20161114_1407.vcf.gz), (RodBinding name=variant19 source=/seq/tng/methodsdev/data/sample_vcf/C1468/Exome/Homo_sapiens_assembly19/04C31949.20161114_1407.vcf.gz), (RodBinding name=variant20 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C30208.20161114_1406.vcf.gz), (RodBinding name=variant21 source=/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/04C30211.20161114_1407.vcf.gz), (RodBinding name=variant22 source=/seq/tng/methodsdev/data/sample_vcf/D5301/Exome/Homo_sapiens_assembly19/NA12878.20161111_1044.vcf.gz), (RodBinding name=variant23 source=/seq/tng/methodsdev/data/sample_vcf/D5301/Exome/Homo_sapiens_assembly19/NA12892.20161111_1044.vcf.gz), (RodBinding name=variant24 source=/seq/tng/methodsdev/data/sample_vcf/D5301/Exome/Homo_sapiens_assembly19/NA12891.20161111_1044.vcf.gz)])] out=/humgen/gsa-hpprojects/dev/gauthier/medianRankSum/multiSamples.g.vcf convertToBasePairResolution=false breakBandsAtMultiplesOf=0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.6-81-gfa572ca,Date="Tue Nov 15 02:20:42 EST 2016",Epoch=1479194442899,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/seq/picard_aggregation/C1710/04C29912/v2/04C29912.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/seq/tng/methodsdev/pod/pod2temp/temp/seq/tng/methodsdev/data/sample_vcf/C1710/Exome/Homo_sapiens_assembly19/91eab078-e8dd-3f64-92e3-f35325aa70e3/scattered/temp_0001_of_10/scattered.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=true no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[AS_Standard, Standard, StandardHC, BetaTesting] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 max_alternate_alleles=3 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=2.0E-4 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf6681670462135264020.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --annotation ClippingRankSumTest --annotation-group AS_StandardAnnotation --annotation-group StandardAnnotation --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="August 2, 2019 3:57:32 PM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
 ##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
 ##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
 ##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient">
 ##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
 ##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
@@ -136,10 +136,9 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA12891	NA12892	Sample1	Sample10	Sample11	Sample12	Sample13	Sample14	Sample15	Sample16	Sample17	Sample18	Sample19	Sample2	Sample20	Sample21	Sample3	Sample4	Sample5	Sample6	Sample7	Sample8	Sample9
-20	899928	.	G	C	4973.06	.	AC=21;AF=0.808;AN=26;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_InbreedingCoeff=0.5339;AS_MQ=43.54;AS_MQRankSum=-0.700;AS_QD=25.36;AS_ReadPosRankSum=0.000;AS_SOR=1.863;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=133;ExcessHet=0.0570;FS=0.000;InbreedingCoeff=0.4870;MLEAC=29;MLEAF=1.00;MQ=42.34;MQRankSum=-6.740e-01;QD=28.73;RAW_MQ=222270.00;ReadPosRankSum=0.00;SOR=1.781	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,18:18:54:1|1:899928_G_C:767,54,0	1/1:0,15:15:45:1|1:899928_G_C:640,45,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0	./.:0,0	1/1:0,9:9:27:1|1:899928_G_C:370,27,0	1/1:0,1:1:3:1|1:899928_G_C:45,3,0	./.:1,0:1:.:.:.:0,0,0	./.:2,0:2:.:.:.:0,0,0	./.:3,0:3:.:.:.:0,0,0	1/1:0,5:5:15:1|1:899928_G_C:225,15,0	./.:0,0	0/1:2,2:4:78:0|1:899928_G_C:78,0,282	./.:0,0:0:.:.:.:0,0,0	1/1:0,51:51:99:1|1:899928_G_C:2229,153,0	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	./.:2,0:2:.:.:.:0,0,0	0/0:7,0:7:21:.:.:0,21,236	1/1:0,4:4:12:1|1:899928_G_C:168,12,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.:0,0:0:.:.:.:0,0,0	0/0:2,0:2:6:.:.:0,6,65
+20	899928	.	G	C	4973.12	.	AC=21;AF=0.808;AN=26;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_InbreedingCoeff=0.5339;AS_MQ=43.54;AS_MQRankSum=-0.700;AS_QD=25.36;AS_ReadPosRankSum=0.000;AS_SOR=1.863;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=133;ExcessHet=0.0570;FS=0.000;InbreedingCoeff=0.4870;MLEAC=29;MLEAF=1.00;MQ=42.34;MQRankSum=-6.740e-01;QD=28.73;RAW_MQ=222270.00;ReadPosRankSum=0.00;SOR=1.781	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,18:18:54:1|1:899928_G_C:767,54,0	1/1:0,15:15:45:1|1:899928_G_C:640,45,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0	./.:0,0	1/1:0,9:9:27:1|1:899928_G_C:370,27,0	1/1:0,1:1:3:1|1:899928_G_C:45,3,0	./.:1,0:1:.:.:.:0,0,0	./.:2,0:2:.:.:.:0,0,0	./.:3,0:3:.:.:.:0,0,0	1/1:0,5:5:15:1|1:899928_G_C:225,15,0	./.:0,0	0/1:2,2:4:78:0|1:899928_G_C:78,0,282	./.:0,0:0:.:.:.:0,0,0	1/1:0,51:51:99:1|1:899928_G_C:2229,153,0	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	./.:2,0:2:.:.:.:0,0,0	0/0:7,0:7:21:.:.:0,21,236	1/1:0,4:4:12:1|1:899928_G_C:168,12,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.:0,0:0:.:.:.:0,0,0	0/0:2,0:2:6:.:.:0,6,65
 20	899933	.	GGGGGGCGC	G	31.97	.	AC=2;AF=0.063;AN=32;AS_BaseQRankSum=.;AS_FS=0.000;AS_InbreedingCoeff=0.2616;AS_MQ=60.00;AS_MQRankSum=.;AS_QD=30.97;AS_ReadPosRankSum=.;AS_SOR=0.693;DP=128;ExcessHet=0.0706;FS=0.000;InbreedingCoeff=0.4045;MLEAC=2;MLEAF=0.063;MQ=34.64;QD=31.97;RAW_MQ=3600.00;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/0:3,0:3:9:.:.:0,9,97	0/0:18,0:18:27:.:.:0,27,405	0/0:15,0:15:24:.:.:0,24,360	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0	./.:0,0	0/0:8,0:8:21:.:.:0,21,315	1/1:0,1:1:3:1|1:899928_G_C:45,3,0	0/0:1,0:1:3:.:.:0,3,33	./.:2,0:2:.:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,34	0/0:6,0:6:15:.:.:0,15,225	./.:0,0	0/0:4,0:4:9:.:.:0,9,135	./.:0,0:0:.:.:.:0,0,0	0/0:52,0:52:99:.:.:0,120,1800	0/0:3,0:3:9:.:.:0,9,115	0/0:2,0:2:3:.:.:0,3,45	0/0:6,0:6:15:.:.:0,15,225	0/0:3,0:3:6:.:.:0,6,90	0/0:2,0:2:6:.:.:0,6,77	./.:0,0:0:.:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,36
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-20	899942	.	G	A	4913.72	.	AC=19;AF=0.792;AN=24;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_InbreedingCoeff=0.5567;AS_MQ=44.39;AS_MQRankSum=-0.300;AS_QD=30.62;AS_ReadPosRankSum=-1.500;AS_SOR=1.893;BaseQRankSum=0.493;ClippingRankSum=0.00;DP=148;ExcessHet=0.0680;FS=0.000;InbreedingCoeff=0.4850;MLEAC=30;MLEAF=1.00;MQ=43.13;MQRankSum=-2.530e-01;QD=28.17;RAW_MQ=264157.00;ReadPosRankSum=-1.501e+00;SOR=1.923	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,15:15:45:1|1:899928_G_C:636,45,0	1/1:0,16:16:45:1|1:899928_G_C:636,45,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0	./.:1,0:1:.:.:.:0,0,0	1/1:0,9:9:27:1|1:899928_G_C:366,27,0	./.:3,0:3:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:2,0:2:.:.:.:0,0,0	./.:1,0:1:.:.:.:0,0,0	1/1:0,7:7:19:1|1:899928_G_C:273,19,0	./.:0,0	0/1:2,8:10:88:0|1:899928_G_C:88,0,274	./.:0,0:0:.:.:.:0,0,0	1/1:0,58:58:99:1|1:899928_G_C:2217,159,0	1/1:0,5:5:13:1|1:899928_G_C:183,13,0	./.:2,0:2:.:.:.:0,0,0	0/0:5,0:5:15:.:.:0,15,178	1/1:0,7:7:16:1|1:899928_G_C:189,16,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.:0,0:0:.:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,36
+20	899937	.	G	T,*	4886.09	.	AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.000,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5390,0.3914;AS_MQ=40.57,0.00;AS_MQRankSum=-0.700,.;AS_QD=27.24,16.50;AS_ReadPosRankSum=0.000,.;AS_SOR=1.775,0.105;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=126;ExcessHet=0.0570;FS=0.000;InbreedingCoeff=0.5260;MLEAC=29,2;MLEAF=1.00,0.077;MQ=39.50;MQRankSum=-6.740e-01;QD=28.20;RAW_MQ=184116.00;ReadPosRankSum=0.00;SOR=1.697	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135	1/1:0,15,0:15:45:1|1:899928_G_C:675,45,0,675,45,675	1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	./.:0,0,0	./.:1,0,0:1:.:.:.:0,0,0,0,0,0	1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360	2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0	./.:1,0,0:1:.:.:.:0,0,0,0,0,0	./.:2,0,0:2:.:.:.:0,0,0,0,0,0	./.:1,0,0:1:.:.:.:0,0,0,0,0,0	1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270	./.:0,0,0	0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	./.:2,0,0:2:.:.:.:0,0,0,0,0,0	0/0:7,0,0:7:9:.:.:0,9,182,9,182,182	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	0/0:1,0,0:1:3:.:.:0,3,36,3,36,36
+20	899938	.	G	C,*	4882.54	.	AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.400,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5553,0.4090;AS_MQ=40.66,0.00;AS_MQRankSum=-0.700,.;AS_QD=25.00,16.50;AS_ReadPosRankSum=0.000,.;AS_SOR=1.900,0.105;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=124;ExcessHet=0.0570;FS=0.000;InbreedingCoeff=0.5362;MLEAC=29,2;MLEAF=1.00,0.077;MQ=39.58;MQRankSum=-6.740e-01;QD=29.56;RAW_MQ=183275.00;ReadPosRankSum=0.00;SOR=1.811	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135	1/1:0,14,0:14:45:1|1:899928_G_C:675,45,0,675,45,675	1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	./.:0,0,0	./.:1,0,0:1:.:.:.:0,0,0,0,0,0	1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360	2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0	./.:1,0,0:1:.:.:.:0,0,0,0,0,0	./.:2,0,0:2:.:.:.:0,0,0,0,0,0	./.:1,0,0:1:.:.:.:0,0,0,0,0,0	1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270	./.:0,0,0	0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	./.:2,0,0:2:.:.:.:0,0,0,0,0,0	0/0:6,0,0:6:15:.:.:0,15,225,15,225,225	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90	./.:0,0,0:0:.:.:.:0,0,0,0,0,0	0/0:1,0,0:1:3:.:.:0,3,36,3,36,36
+20	899942	.	G	A	4913.79	.	AC=19;AF=0.792;AN=24;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_InbreedingCoeff=0.5567;AS_MQ=44.39;AS_MQRankSum=-0.300;AS_QD=30.62;AS_ReadPosRankSum=-1.500;AS_SOR=1.893;BaseQRankSum=0.493;ClippingRankSum=0.00;DP=148;ExcessHet=0.0680;FS=0.000;InbreedingCoeff=0.4850;MLEAC=30;MLEAF=1.00;MQ=43.13;MQRankSum=-2.530e-01;QD=28.17;RAW_MQ=264157.00;ReadPosRankSum=-1.501e+00;SOR=1.923	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,15:15:45:1|1:899928_G_C:636,45,0	1/1:0,16:16:45:1|1:899928_G_C:636,45,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:0,0	./.:1,0:1:.:.:.:0,0,0	1/1:0,9:9:27:1|1:899928_G_C:366,27,0	./.:3,0:3:.:.:.:0,0,0	./.:0,0:0:.:.:.:0,0,0	./.:2,0:2:.:.:.:0,0,0	./.:1,0:1:.:.:.:0,0,0	1/1:0,7:7:19:1|1:899928_G_C:273,19,0	./.:0,0	0/1:2,8:10:88:0|1:899928_G_C:88,0,274	./.:0,0:0:.:.:.:0,0,0	1/1:0,58:58:99:1|1:899928_G_C:2217,159,0	1/1:0,5:5:13:1|1:899928_G_C:183,13,0	./.:2,0:2:.:.:.:0,0,0	0/0:5,0:5:15:.:.:0,15,178	1/1:0,7:7:16:1|1:899928_G_C:189,16,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.:0,0:0:.:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,36
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ndaTest.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ndaTest.gatk3.7_30_ga4f720357.expected.vcf
index 2ca559cbf71..8c9e76720ff 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ndaTest.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ndaTest.gatk3.7_30_ga4f720357.expected.vcf
@@ -8,7 +8,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/ndaTest.gatk3.7_30_ga4f720357.expected.vcf --annotate-with-num-discovered-alleles true --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:15 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -114,78 +113,77 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	.	C	T	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.110e-01;DP=38;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.172e+00;NDA=1;QD=16.67;ReadPosRankSum=-2.350e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
-20	10000211	.	C	T	659.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;ClippingRankSum=-1.927e+00;DP=42;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.89;MQ0=0;MQRankSum=-1.750e+00;NDA=1;QD=15.70;ReadPosRankSum=1.55;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
-20	10000439	.	T	G	1757.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.41;MQ0=0;NDA=1;QD=31.38;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
-20	10000598	.	T	A	1774.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.55;MQ0=0;NDA=1;QD=33.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
-20	10000694	.	G	A	982.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-9.000e-03;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.482;NDA=1;QD=18.54;ReadPosRankSum=1.54;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
-20	10000758	.	T	A	1683.03	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;NDA=1;QD=33.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1697,149,0
-20	10001019	.	T	G	114.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;ClippingRankSum=-3.470e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.65;MQ0=0;MQRankSum=-9.250e-01;NDA=1;QD=4.41;ReadPosRankSum=0.00;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
-20	10001298	.	T	A	1424.03	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=171.56;MQ0=0;NDA=1;QD=34.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
-20	10001436	.	A	AAGGCT	1872.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;NDA=1;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
-20	10001474	.	C	T	1614.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;NDA=1;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
-20	10001617	.	C	A	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=-8.430e-01;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.345e+00;NDA=1;QD=16.67;ReadPosRankSum=-2.810e-01;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
-20	10001628	.	G	A	1387.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;NDA=1;QD=30.97;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
-20	10001661	.	T	C	1559.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.28;MQ0=0;NDA=1;QD=27.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1573,108,0
-20	10001670	.	T	G	1559.03	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.63;MQ0=0;NDA=1;QD=28.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,32:32:99:1573,108,0
-20	10002058	.	T	G	1722.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;NDA=1;QD=25.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
-20	10002099	.	C	T	614.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.583e+00;DP=50;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.61;MQ0=0;MQRankSum=-1.719e+00;NDA=1;QD=12.29;ReadPosRankSum=1.85;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
-20	10002138	.	C	G	2143.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.52;MQ0=0;NDA=1;QD=29.56;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2157,147,0
-20	10002142	.	G	C	2143.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.31;MQ0=0;NDA=1;QD=30.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2157,147,0
-20	10002458	.	G	GTT,GTTT	1170.10	.	AC=1,1;AF=0.500,0.500;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=186.78;MQ0=0;NDA=2;QD=28.17;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,8,7:15:99:1187,229,144,270,0,185
-20	10002470	.	C	T	1218.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=179.57;MQ0=0;NDA=1;QD=26.80;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,29:29:86:1232,86,0
-20	10002625	.	G	T	1339.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;NDA=1;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
-20	10003021	.	C	T	1393.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=214.87;MQ0=0;NDA=1;QD=34.83;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
-20	10003358	.	A	C	377.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.209;ClippingRankSum=0.095;DP=32;ExcessHet=3.0103;FS=3.270;MLEAC=1;MLEAF=0.500;MQ=224.98;MQ0=0;MQRankSum=-1.710e-01;NDA=1;QD=11.80;ReadPosRankSum=1.12;SOR=1.445	GT:AD:DP:GQ:PL	0/1:18,14:32:99:385,0,504
-20	10003651	.	T	C	1401.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;NDA=1;QD=26.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
-20	10003692	.	A	G	1602.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.51;MQ0=0;NDA=1;QD=34.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1616,141,0
-20	10003832	.	G	A	1874.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.45;MQ0=0;NDA=1;QD=34.07;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,55:55:99:1888,165,0
-20	10004094	.	A	C	943.03	.	AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=101.97;MQ0=0;NDA=1;QD=31.43;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:957,90,0
-20	10004147	.	A	G	559.03	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;NDA=1;QD=24.31;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,23:23:66:573,66,0
-20	10004193	.	G	T	294.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.124;ClippingRankSum=-2.060e-01;DP=20;ExcessHet=3.0103;FS=9.556;MLEAC=1;MLEAF=0.500;MQ=86.94;MQ0=0;MQRankSum=0.289;NDA=1;QD=15.51;ReadPosRankSum=-1.197e+00;SOR=3.442	GT:AD:DP:GQ:PL	0/1:8,11:19:99:302,0,223
-20	10004222	.	C	CA	312.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.460e-01;ClippingRankSum=1.08;DP=27;ExcessHet=3.0103;FS=14.428;MLEAC=1;MLEAF=0.500;MQ=143.03;MQ0=0;MQRankSum=-2.770e-01;NDA=1;QD=13.59;ReadPosRankSum=-3.390e-01;SOR=0.969	GT:AD:DP:GQ:PL	0/1:12,11:23:99:320,0,341
-20	10004223	.	A	AG	283.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.90;ClippingRankSum=-1.642e+00;DP=31;ExcessHet=3.0103;FS=14.989;MLEAC=1;MLEAF=0.500;MQ=152.05;MQ0=0;MQRankSum=0.264;NDA=1;QD=9.15;ReadPosRankSum=1.36;SOR=2.640	GT:AD:DP:GQ:PL	0/1:19,12:31:99:291,0,501
-20	10004351	.	C	G	1638.03	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.76;MQ0=0;NDA=1;QD=30.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1652,132,0
-20	10004389	.	T	G	1896.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.38;MQ0=0;NDA=1;QD=31.98;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1910,156,0
-20	10004610	.	A	C	1600.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.18;MQ0=0;NDA=1;QD=32.65;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1614,146,0
-20	10004725	.	A	G	602.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.44;ClippingRankSum=-5.850e-01;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.84;MQ0=0;MQRankSum=1.95;NDA=1;QD=12.82;ReadPosRankSum=0.649;SOR=0.784	GT:AD:DP:GQ:PL	0/1:24,23:47:99:610,0,600
+20	10000117	.	C	T	633.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.110e-01;DP=38;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.172e+00;NDA=1;QD=16.67;ReadPosRankSum=-2.350e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
+20	10000211	.	C	T	659.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;ClippingRankSum=-1.927e+00;DP=42;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.89;MQ0=0;MQRankSum=-1.750e+00;NDA=1;QD=15.71;ReadPosRankSum=1.55;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
+20	10000439	.	T	G	1757.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.41;MQ0=0;NDA=1;QD=31.38;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
+20	10000598	.	T	A	1774.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.55;MQ0=0;NDA=1;QD=33.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
+20	10000694	.	G	A	982.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-9.000e-03;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.482;NDA=1;QD=18.54;ReadPosRankSum=1.54;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
+20	10000758	.	T	A	1683.06	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;NDA=1;QD=33.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1697,149,0
+20	10001019	.	T	G	114.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;ClippingRankSum=-3.470e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.65;MQ0=0;MQRankSum=-9.250e-01;NDA=1;QD=4.41;ReadPosRankSum=0.00;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
+20	10001298	.	T	A	1424.06	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=171.56;MQ0=0;NDA=1;QD=34.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
+20	10001436	.	A	AAGGCT	1872.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;NDA=1;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
+20	10001474	.	C	T	1614.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;NDA=1;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
+20	10001617	.	C	A	633.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=-8.430e-01;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.345e+00;NDA=1;QD=16.67;ReadPosRankSum=-2.810e-01;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
+20	10001628	.	G	A	1387.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;NDA=1;QD=30.97;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
+20	10001661	.	T	C	1559.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.28;MQ0=0;NDA=1;QD=27.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1573,108,0
+20	10001670	.	T	G	1559.06	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.63;MQ0=0;NDA=1;QD=28.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,32:32:99:1573,108,0
+20	10002058	.	T	G	1722.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;NDA=1;QD=25.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
+20	10002099	.	C	T	614.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;ClippingRankSum=-1.583e+00;DP=50;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.61;MQ0=0;MQRankSum=-1.719e+00;NDA=1;QD=12.29;ReadPosRankSum=1.85;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
+20	10002138	.	C	G	2143.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.52;MQ0=0;NDA=1;QD=29.56;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2157,147,0
+20	10002142	.	G	C	2143.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.31;MQ0=0;NDA=1;QD=30.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:2157,147,0
+20	10002458	.	G	GTT,GTTT	1170.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=186.78;MQ0=0;NDA=2;QD=28.17;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,8,7:15:99:1187,229,144,270,0,185
+20	10002470	.	C	T	1218.06	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=179.57;MQ0=0;NDA=1;QD=26.80;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,29:29:86:1232,86,0
+20	10002625	.	G	T	1339.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;NDA=1;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
+20	10003021	.	C	T	1393.06	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=214.87;MQ0=0;NDA=1;QD=34.83;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
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+20	10003651	.	T	C	1401.06	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;NDA=1;QD=26.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
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+20	10004147	.	A	G	559.06	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;NDA=1;QD=24.31;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,23:23:66:573,66,0
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+20	10004610	.	A	C	1600.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.18;MQ0=0;NDA=1;QD=32.65;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1614,146,0
+20	10004725	.	A	G	602.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.44;ClippingRankSum=-5.850e-01;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.84;MQ0=0;MQRankSum=1.95;NDA=1;QD=12.82;ReadPosRankSum=0.649;SOR=0.784	GT:AD:DP:GQ:PL	0/1:24,23:47:99:610,0,600
 20	10004769	.	TAAAACTATGC	T	675.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.710e-01;ClippingRankSum=-5.370e-01;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.95;MQ0=0;MQRankSum=-4.022e+00;NDA=1;QD=15.35;ReadPosRankSum=0.585;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:683,0,2740
-20	10004874	.	A	C	1701.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.94;MQ0=0;NDA=1;QD=34.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1715,150,0
-20	10004887	.	A	G	579.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.979;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=222.04;MQ0=0;MQRankSum=-3.733e+00;NDA=1;QD=12.33;ReadPosRankSum=1.02;SOR=0.813	GT:AD:DP:GQ:PL	0/1:27,20:47:99:587,0,796
-20	10005010	.	C	T	1376.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=225.36;MQ0=0;NDA=1;QD=27.51;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
-20	10005427	.	C	T	1839.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;NDA=1;QD=34.06;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
-20	10005499	.	A	G	1798.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.64;ClippingRankSum=-4.720e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.00;NDA=1;QD=32.69;ReadPosRankSum=1.91;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1812,116,0
-20	10005587	.	A	G	821.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;ClippingRankSum=-1.027e+00;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-1.724e+00;NDA=1;QD=15.50;ReadPosRankSum=0.348;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
-20	10005723	.	A	G	1461.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;NDA=1;QD=31.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
-20	10006291	.	G	A	456.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;NDA=1;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
-20	10006404	.	A	C	1438.03	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.10;MQ0=0;NDA=1;QD=31.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1452,135,0
-20	10006682	.	T	A	1005.03	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;NDA=1;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
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+20	10005587	.	A	G	821.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;ClippingRankSum=-1.027e+00;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-1.724e+00;NDA=1;QD=15.50;ReadPosRankSum=0.348;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
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+20	10006291	.	G	A	456.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;NDA=1;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
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+20	10006682	.	T	A	1005.06	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;NDA=1;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
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-20	10007150	.	G	C	537.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;NDA=1;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
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-20	10007352	.	C	T	1476.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;NDA=1;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
-20	10007531	.	A	G	1654.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;NDA=1;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
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-20	10008029	.	T	TA	1505.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;NDA=1;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
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+20	10007352	.	C	T	1476.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;NDA=1;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
+20	10007531	.	A	G	1654.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;NDA=1;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
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+20	10008029	.	T	TA	1505.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;NDA=1;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
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-20	10008221	.	T	C	1822.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;NDA=1;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
-20	10008458	.	T	G	1627.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;NDA=1;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
-20	10008742	.	G	T	218.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.16;ClippingRankSum=1.35;DP=19;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=106.06;MQ0=0;MQRankSum=0.694;NDA=1;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
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-20	10008921	.	C	CA	356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;NDA=1;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
+20	10008221	.	T	C	1822.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;NDA=1;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
+20	10008458	.	T	G	1627.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;NDA=1;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
+20	10008742	.	G	T	218.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.16;ClippingRankSum=1.35;DP=19;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=106.06;MQ0=0;MQRankSum=0.694;NDA=1;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
+20	10008758	.	C	CA	491.03	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;NDA=1;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
+20	10008921	.	C	CA	356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;NDA=1;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
 20	10008948	.	TA	T	1057.03	.	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=168.45;MQ0=0;NDA=1;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
-20	10008952	.	CACACACACACA	C,CCACACACACA	988.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;NDA=2;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
-20	10009227	.	A	G	875.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;NDA=1;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
-20	10009246	.	A	G	2043.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;NDA=1;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
-20	10009400	.	T	A	1620.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;NDA=1;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
-20	10009512	.	C	G	1516.03	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;NDA=1;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
-20	10009719	.	A	G	1091.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;NDA=1;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
-20	10009795	.	A	G	1171.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;NDA=1;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
-20	10009842	.	G	GAA	383.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;NDA=1;QD=14.76;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
-20	10009844	.	G	A	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;NDA=1;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
-20	10009871	.	A	G	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;NDA=1;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10008952	.	CACACACACACA	C,CCACACACACA	988.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;NDA=2;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
+20	10009227	.	A	G	875.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;NDA=1;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
+20	10009246	.	A	G	2043.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;NDA=1;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
+20	10009400	.	T	A	1620.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;NDA=1;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
+20	10009512	.	C	G	1516.06	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;NDA=1;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
+20	10009719	.	A	G	1091.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;NDA=1;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
+20	10009795	.	A	G	1171.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;NDA=1;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
+20	10009842	.	G	GAA	383.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;NDA=1;QD=14.75;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
+20	10009844	.	G	A	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;NDA=1;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10009871	.	A	G	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;NDA=1;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
 20	10009875	.	A	G,AGGGAGG	1479.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=192.36;MQ0=0;NDA=3;QD=26.61;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,14,11:25:99:1496,567,1162,680,0,1286
-20	10009879	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;NDA=1;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
-20	10009883	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;NDA=1;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
+20	10009879	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;NDA=1;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
+20	10009883	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;NDA=1;QD=28.55;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf
index 4e574e43f9b..1d38c983824 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/emeryj/hellbender/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf --variant /Users/emeryj/hellbender/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf --reference /Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-vcf-codec false --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="August 13, 2020 10:36:17 AM EDT">
 ##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller  --emit-ref-confidence GVCF --output YRIoffspring.chr20snippet.g.vcf --intervals 20:10000000-10100000 --input /seq/picard_aggregation/G96830/NA19240/v1/NA19240.bam --reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta  --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --disable-tool-default-annotations false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20",Version=4.0.4.0-52-g41c08ad-SNAPSHOT,Date="June 12, 2018 9:01:56 AM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
@@ -116,7 +115,6 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=GRCh37>
 ##contig=<ID=GL000192.1,length=547496,assembly=GRCh37>
 ##contig=<ID=NC_007605,length=171823,assembly=NC_007605.1>
-##source=GenotypeGVCFs
 ##source=HaplotypeCaller
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
 20	10000117	.	C	T	925.91	.	AC=1;AF=0.250;AN=4;BaseQRankSum=2.14;DP=109;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.250;MQ=59.72;MQRankSum=0.913;QD=14.47;ReadPosRankSum=-2.230e-01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248	0/0:43,0:43:99:0,109,1311
@@ -339,8 +337,8 @@
 20	10067264	.	G	A	3256.13	.	AC=3;AF=0.750;AN=4;BaseQRankSum=0.369;ClippingRankSum=0.00;DP=106;ExcessHet=3.0103;FS=3.400;MLEAC=3;MLEAF=0.750;MQ=59.56;MQRankSum=0.00;QD=30.72;ReadPosRankSum=-4.930e-01;SOR=0.518	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0	0/1:20,13:33:99:319,0,534
 20	10067722	.	A	C	3344.13	.	AC=4;AF=1.00;AN=4;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=34.66;SOR=0.782	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0	1/1:0,38:38:99:1185,114,0
 20	10068158	.	GTGTATATATATA	G	96.88	.	AC=1;AF=0.250;AN=4;BaseQRankSum=-8.420e-01;DP=59;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.250;MQ=56.62;MQRankSum=0.328;QD=13.84;ReadPosRankSum=0.524;SOR=0.061	GT:AD:DP:GQ:PL	0/1:3,4:7:57:105,0,57	0/0:31,0:31:54:0,54,810
-20	10068160	.	GTATATATATATGTA	G,*	87.21	.	AC=1,1;AF=0.250,0.250;AN=4;DP=64;ExcessHet=0.7918;FS=0.000;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.29;QD=14.54;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53	0/0:32,0,0:32:45:0,45,675,45,675,675
-20	10068166	.	ATATATG	A,*	244.81	.	AC=1,2;AF=0.250,0.500;AN=4;BaseQRankSum=-9.800e-01;ClippingRankSum=0.00;DP=57;ExcessHet=3.0103;FS=8.113;MLEAC=1,2;MLEAF=0.250,0.500;MQ=59.33;MQRankSum=0.00;QD=16.32;ReadPosRankSum=-6.600e-01;SOR=1.245	GT:AD:DP:GQ:PGT:PID:PL:PS	2/2:0,0,4:6:45:.:.:653,436,405,45,51,0	0/1:2,9,0:11:22:0|1:10068166_ATATATG_A:218,0,22,224,49,273:10068166
+20	10068160	.	GTATATATATATGTA	G,*	56.01	.	AC=1,1;AF=0.250,0.250;AN=4;DP=64;ExcessHet=0.7918;FS=0.000;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.29;QD=9.33;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:706,158,131,98,0,53	0/0:32,0,0:32:45:0,45,675,45,675,675
+20	10068166	.	ATATATG	A,*	210.22	.	AC=1,2;AF=0.250,0.500;AN=4;BaseQRankSum=-9.800e-01;ClippingRankSum=0.00;DP=57;ExcessHet=3.0103;FS=8.113;MLEAC=1,2;MLEAF=0.250,0.500;MQ=59.33;MQRankSum=0.00;QD=14.01;ReadPosRankSum=-6.600e-01;SOR=1.245	GT:AD:DP:GQ:PGT:PID:PL:PS	2/2:0,0,4:6:45:.:.:653,436,405,45,51,0	0/1:2,9,0:11:22:0|1:10068166_ATATATG_A:218,0,22,224,49,273:10068166
 20	10068981	.	G	A	3361.13	.	AC=4;AF=1.00;AN=4;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=29.40;SOR=0.812	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0	1/1:0,26:26:78:845,78,0
 20	10070602	.	T	C	3181.13	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-3.081e+00;ClippingRankSum=0.00;DP=116;ExcessHet=3.0103;FS=4.673;MLEAC=3;MLEAF=0.750;MQ=59.20;MQRankSum=0.00;QD=28.40;ReadPosRankSum=-6.890e-01;SOR=0.377	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0	0/1:21,19:40:99:475,0,592
 20	10070936	.	T	A	4371.13	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.071e+00;ClippingRankSum=0.00;DP=127;ExcessHet=3.0103;FS=1.983;MLEAC=3;MLEAF=0.750;MQ=59.30;MQRankSum=0.00;QD=36.76;ReadPosRankSum=0.014;SOR=0.489	GT:AD:DP:GQ:PGT:PID:PL:PS	1|1:0,82:82:99:1|1:10070936_T_A:3660,247,0:10070936	0/1:21,19:40:99:0|1:10070936_T_A:725,0,1215:10070936
@@ -439,7 +437,7 @@
 20	10097075	.	T	G	2516.13	.	AC=3;AF=0.750;AN=4;BaseQRankSum=1.82;ClippingRankSum=0.00;DP=130;ExcessHet=3.0103;FS=5.781;MLEAC=3;MLEAF=0.750;MQ=58.63;MQRankSum=0.00;QD=19.97;ReadPosRankSum=1.53;SOR=0.480	GT:AD:DP:GQ:PL	0/1:44,48:92:99:1474,0,1482	1/1:1,33:34:92:1056,92,0
 20	10097101	.	C	CTTTT,CTTT	2117.80	.	AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.195e+00;DP=109;ExcessHet=3.0103;FS=3.013;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.55;MQRankSum=-2.391e+00;QD=24.92;ReadPosRankSum=2.40;SOR=0.385	GT:AD:DP:GQ:PL	0/2:33,4,26:63:99:1132,558,1784,0,1200,1217	1/1:0,22,0:22:71:1008,71,0,1008,71,1009
 20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C	1080.88	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.65;DP=120;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.250;MQ=54.34;MQRankSum=-6.464e+00;QD=12.14;ReadPosRankSum=-3.097e+00;SOR=0.948	GT:AD:DP:GQ:PL	0/1:57,32:89:99:1089,0,2243	0/0:30,0:30:66:0,66,990
-20	10097437	.	TTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC	*,TTTTCTTTCTTTCTTTCTTTCTTTCTTTC,T	1842.24	.	AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=55.51;QD=24.24;SOR=1.905	GT:AD:DP:GQ:PL	1/2:0,32,23,0:55:99:2123,939,1800,1192,0,1122,2197,1454,1259,2640	3/3:0,0,0,21:21:67:928,928,928,928,928,928,67,67,67,0
+20	10097437	.	TTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC	*,TTTTCTTTCTTTCTTTCTTTCTTTCTTTC,T	1842.20	.	AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=55.51;QD=24.24;SOR=1.905	GT:AD:DP:GQ:PL	1/2:0,32,23,0:55:99:2123,939,1800,1192,0,1122,2197,1454,1259,2640	3/3:0,0,0,21:21:67:928,928,928,928,928,928,67,67,67,0
 20	10097626	.	C	A	646.91	.	AC=1;AF=0.250;AN=4;BaseQRankSum=1.09;DP=83;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.250;MQ=58.00;MQRankSum=-1.331e+00;QD=13.48;ReadPosRankSum=1.02;SOR=0.324	GT:AD:DP:GQ:PL	0/1:28,20:48:99:655,0,957	0/0:29,0:29:81:0,81,1014
 20	10097751	.	T	C	978.48	.	AC=2;AF=0.500;AN=4;BaseQRankSum=-3.680e-01;ClippingRankSum=0.00;DP=87;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.75;ReadPosRankSum=1.08;SOR=0.350	GT:AD:DP:GQ:PL	0/0:49,0:49:99:0,120,1800	1/1:1,37:38:82:994,82,0
 20	10097789	.	T	C	2033.13	.	AC=3;AF=0.750;AN=4;BaseQRankSum=-1.157e+00;DP=103;ExcessHet=3.0103;FS=5.286;MLEAC=3;MLEAF=0.750;MQ=58.67;MQRankSum=-2.805e+00;QD=20.33;ReadPosRankSum=0.220;SOR=0.574	GT:AD:DP:GQ:PL	0/1:34,23:57:99:717,0,1190	1/1:0,43:43:99:1330,129,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx
index 7c8b384676ddce4c32585836cfb50ca93e919fac..312655006e5845f0eef5b8aad0eb6bded4e70270 100644
GIT binary patch
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf
index 683986da94a..0fe07e3fdfc 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Physical phasing set information, identifying the position of the first variant in the phasing group">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/emeryj/hellbender/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf --variant /Users/emeryj/hellbender/gatk/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGVCFMode.gatk4.g.vcf --reference /Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genomicsdb-use-vcf-codec false --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="August 13, 2020 10:36:17 AM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -33,7 +32,6 @@
 ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
 ##contig=<ID=20,length=63025520>
 ##contig=<ID=21,length=48129895>
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
 20	10000117	.	C	T	926.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.14;DP=64;ExcessHet=3.0103;FS=11.007;MLEAC=1;MLEAF=0.500;MQ=59.71;MQRankSum=0.913;QD=14.48;ReadPosRankSum=-2.230e-01;SOR=1.538	GT:AD:DP:GQ:PL	0/1:36,28:64:99:934,0,1248
 20	10000211	.	C	T	962.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;DP=53;ExcessHet=3.0103;FS=5.587;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=1.06;QD=18.16;ReadPosRankSum=0.703;SOR=0.944	GT:AD:DP:GQ:PL	0/1:26,27:53:99:970,0,906
@@ -189,7 +187,7 @@
 20	10067264	.	G	A	2937.06	.	AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=30.49;SOR=0.776	GT:AD:DP:GQ:PL	1/1:0,73:73:99:2951,219,0
 20	10067722	.	A	C	2161.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.67;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:2175,163,0
 20	10068158	.	GTGTATATATATA	G	96.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.520e-01;DP=29;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=56.74;MQRankSum=0.328;QD=13.80;ReadPosRankSum=0.524;SOR=0.061	GT:AD:DP:GQ:PL	0/1:3,4:7:57:104,0,57
-20	10068160	.	GTATATATATATGTA	G,*	92.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.74;QD=15.33;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:735,162,131,102,0,53
+20	10068160	.	GTATATATATATGTA	G,*	56.01	.	AC=1,1;AF=0.500,0.500;AN=2;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.74;QD=9.33;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,2,4:6:53:735,162,131,102,0,53
 20	10068981	.	G	A	2518.06	.	AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.53;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2532,184,0
 20	10070602	.	T	C	2706.06	.	AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.71;QD=32.63;SOR=0.749	GT:AD:DP:GQ:PL	1/1:0,72:72:99:2720,216,0
 20	10070936	.	T	A	3646.06	.	AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;QD=30.36;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL:PS	1|1:0,81:81:99:1|1:10070936_T_A:3660,247,0:10070936
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf
index 36b45ad547f..ed3441a4f85 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.2
 ##ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">
 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -10,7 +11,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.combined.g.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:16 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -114,7 +114,6 @@
 ##contig=<ID=NC_007605,length=171823>
 ##contig=<ID=hs37d5,length=35477943>
 ##reference=file:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1	NA2
 20	69511	.	ACAC	A	2268.44	.	AC=2;AF=0.500;AN=4;DP=162;ExcessHet=0.7918;FS=3.716;MLEAC=2;MLEAF=0.500;QD=28.36;SOR=0.771	GT:AD:DP:GQ:MIN_GQ:PL	1/1:1,79:80:99:.:2284,207,0	0/0:82,0:82:99:99:0,122,1802
-20	69513	.	A	G,*	2415.89	.	AC=2,2;AF=0.500,0.500;AN=4;DP=160;ExcessHet=3.0103;FS=7.469;MLEAC=2,2;MLEAF=0.500,0.500;QD=15.10;SOR=0.712	GT:AD:DP:GQ:PL	2/2:1,0,79:80:99:2284,2287,2316,207,237,0	1/1:1,79,0:80:99:2233,233,0,2244,234,2333
+20	69513	.	A	G,*	2218.93	.	AC=2,2;AF=0.500,0.500;AN=4;DP=160;ExcessHet=3.0103;FS=7.469;MLEAC=2,2;MLEAF=0.500,0.500;QD=13.87;SOR=0.712	GT:AD:DP:GQ:PL	2/2:1,0,79:80:99:2284,2287,2316,207,237,0	1/1:1,79,0:80:99:2233,233,0,2244,234,2333
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf
index 2c501f48106..96c1ec2f6ad 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.delOnly.g.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:16 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -118,5 +117,4 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1	NA2	NA3
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf
index e0c34bc205f..96c1ec2f6ad 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf
@@ -12,7 +12,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/spanningDel.depr.delOnly.g.vcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:16 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -118,5 +117,4 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1	NA2	NA3
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/standardConfTest.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/standardConfTest.gatk3.7_30_ga4f720357.expected.vcf
index 351255f0bff..553451b87ee 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/standardConfTest.gatk3.7_30_ga4f720357.expected.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/standardConfTest.gatk3.7_30_ga4f720357.expected.vcf
@@ -8,7 +8,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/standardConfTest.gatk3.7_30_ga4f720357.expected.vcf --standard-min-confidence-threshold-for-calling 300.0 --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:16 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -113,72 +112,71 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	.	C	T	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-4.110e-01;DP=38;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.172e+00;QD=16.67;ReadPosRankSum=-2.350e-01;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
-20	10000211	.	C	T	659.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;ClippingRankSum=-1.927e+00;DP=42;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.89;MQ0=0;MQRankSum=-1.750e+00;QD=15.70;ReadPosRankSum=1.55;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
-20	10000439	.	T	G	1757.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.41;MQ0=0;QD=31.38;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
-20	10000598	.	T	A	1774.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.55;MQ0=0;QD=33.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
-20	10000694	.	G	A	982.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-9.000e-03;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.482;QD=18.54;ReadPosRankSum=1.54;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
-20	10000758	.	T	A	1683.03	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;QD=33.66;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1697,149,0
-20	10001298	.	T	A	1424.03	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=171.56;MQ0=0;QD=34.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
-20	10001436	.	A	AAGGCT	1872.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
-20	10001474	.	C	T	1614.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;QD=28.73;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
-20	10001617	.	C	A	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=-8.430e-01;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.345e+00;QD=16.67;ReadPosRankSum=-2.810e-01;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
-20	10001628	.	G	A	1387.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;QD=30.97;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
-20	10001661	.	T	C	1559.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.28;MQ0=0;QD=27.24;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1573,108,0
-20	10001670	.	T	G	1559.03	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.63;MQ0=0;QD=28.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,32:32:99:1573,108,0
-20	10002058	.	T	G	1722.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;QD=25.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
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-20	10006291	.	G	A	456.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
-20	10006404	.	A	C	1438.03	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.10;MQ0=0;QD=31.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1452,135,0
-20	10006682	.	T	A	1005.03	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
+20	10004874	.	A	C	1701.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.94;MQ0=0;QD=34.02;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1715,150,0
+20	10004887	.	A	G	579.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.979;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=222.04;MQ0=0;MQRankSum=-3.733e+00;QD=12.33;ReadPosRankSum=1.02;SOR=0.813	GT:AD:DP:GQ:PL	0/1:27,20:47:99:587,0,796
+20	10005010	.	C	T	1376.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=225.36;MQ0=0;QD=31.98;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
+20	10005427	.	C	T	1839.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;QD=34.06;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
+20	10005499	.	A	G	1798.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.64;ClippingRankSum=-4.720e-01;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.00;QD=32.69;ReadPosRankSum=1.91;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1812,116,0
+20	10005587	.	A	G	821.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;ClippingRankSum=-1.027e+00;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-1.724e+00;QD=15.50;ReadPosRankSum=0.348;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
+20	10005723	.	A	G	1461.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;QD=31.09;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
+20	10006291	.	G	A	456.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.683;ClippingRankSum=1.01;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=217.79;MQ0=0;MQRankSum=0.137;QD=10.62;ReadPosRankSum=-8.070e-01;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
+20	10006404	.	A	C	1438.06	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.10;MQ0=0;QD=31.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1452,135,0
+20	10006682	.	T	A	1005.06	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.49;MQ0=0;QD=33.50;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
 20	10006819	.	AAAAC	A	1513.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.67;MQ0=0;QD=27.51;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1527,107,0
-20	10007150	.	G	C	537.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
-20	10007352	.	C	T	1476.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
-20	10007531	.	A	G	1654.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
-20	10007980	.	A	C	1658.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.35;MQ0=0;QD=33.16;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
-20	10008029	.	T	TA	1505.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
+20	10007150	.	G	C	537.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.280e-01;ClippingRankSum=-4.270e-01;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.176;QD=19.91;ReadPosRankSum=0.879;SOR=2.122	GT:AD:DP:GQ:PL	0/1:10,17:27:99:545,0,290
+20	10007352	.	C	T	1476.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.75;MQ0=0;QD=34.33;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1490,129,0
+20	10007531	.	A	G	1654.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
+20	10007980	.	A	C	1658.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.35;MQ0=0;QD=33.16;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
+20	10008029	.	T	TA	1505.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.871e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.54;MQ0=0;MQRankSum=1.92;QD=32.02;ReadPosRankSum=1.87;SOR=0.693	GT:AD:DP:GQ:PL	1/1:2,45:47:70:1519,70,0
 20	10008146	.	TA	T	1727.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.35;MQ0=0;QD=29.11;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1741,142,0
-20	10008221	.	T	C	1822.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
-20	10008458	.	T	G	1627.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
-20	10008758	.	C	CA	491.06	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
-20	10008921	.	C	CA	356.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
+20	10008221	.	T	C	1822.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1836,162,0
+20	10008458	.	T	G	1627.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.62;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1641,141,0
+20	10008758	.	C	CA	491.03	.	AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.12;MQ0=0;QD=32.74;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,15:15:48:505,48,0
+20	10008921	.	C	CA	356.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;ClippingRankSum=0.035;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=144.09;MQ0=0;MQRankSum=0.317;QD=16.98;ReadPosRankSum=-5.990e-01;SOR=0.495	GT:AD:DP:GQ:PL	0/1:10,11:21:99:364,0,269
 20	10008948	.	TA	T	1057.03	.	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=168.45;MQ0=0;QD=28.08;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
-20	10008952	.	CACACACACACA	C,CCACACACACA	988.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
-20	10009227	.	A	G	875.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
-20	10009246	.	A	G	2043.03	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
-20	10009400	.	T	A	1620.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
-20	10009512	.	C	G	1516.03	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
-20	10009719	.	A	G	1091.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
-20	10009795	.	A	G	1171.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
-20	10009842	.	G	GAA	383.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;QD=14.76;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
-20	10009844	.	G	A	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
-20	10009871	.	A	G	532.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10008952	.	CACACACACACA	C,CCACACACACA	988.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=170.70;MQ0=0;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:1005,402,1011,556,0,1362
+20	10009227	.	A	G	875.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.708e+00;ClippingRankSum=-2.827e+00;DP=61;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.94;MQ0=0;MQRankSum=-1.096e+00;QD=14.59;ReadPosRankSum=1.43;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
+20	10009246	.	A	G	2043.06	.	AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.06;MQ0=0;QD=33.49;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2057,183,0
+20	10009400	.	T	A	1620.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.47;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1634,141,0
+20	10009512	.	C	G	1516.06	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
+20	10009719	.	A	G	1091.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.70;MQ0=0;QD=31.17;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
+20	10009795	.	A	G	1171.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=29.03;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
+20	10009842	.	G	GAA	383.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.14;ClippingRankSum=-8.300e-01;DP=38;ExcessHet=3.0103;FS=1.598;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=-8.820e-01;QD=14.75;ReadPosRankSum=0.415;SOR=0.616	GT:AD:DP:GQ:PL	0/1:15,11:26:99:391,0,1301
+20	10009844	.	G	A	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.917e+00;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=188.08;MQ0=0;MQRankSum=1.01;QD=17.18;ReadPosRankSum=0.573;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
+20	10009871	.	A	G	532.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.730e-01;ClippingRankSum=-2.960e-01;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=17.18;ReadPosRankSum=1.09;SOR=0.829	GT:AD:DP:GQ:PL	0/1:16,15:31:99:540,0,1169
 20	10009875	.	A	G,AGGGAGG	1479.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=192.36;MQ0=0;QD=30.67;SOR=0.693	GT:AD:DP:GQ:PL	1/2:0,14,11:25:99:1496,567,1162,680,0,1286
-20	10009879	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;QD=26.61;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
-20	10009883	.	A	G	1580.03	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
+20	10009879	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.98;MQ0=0;QD=26.61;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1594,110,0
+20	10009883	.	A	G	1580.06	.	AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.04;MQ0=0;QD=29.20;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,34:34:99:1594,110,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.expected.g.vcf
index bfbf4344831..1aaab621adc 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.expected.g.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.expected.g.vcf
@@ -13,12 +13,12 @@
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
 ##GATKCommandLine.CombineGVCFs=<ID=CombineGVCFs,Version=3.8-5-g34e1f1e2f,Date="Tue Sep 19 17:40:08 EDT 2017",Epoch=1505857208315,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false annotation=[AS_RMSMappingQuality] dbsnp=(RodBinding name= source=UNBOUND) variant=[(RodBindingCollection [(RodBinding name=variant source=/Users/emeryj/hellbender/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/alleleSpecific/NA12878.AS.chr20snippet.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/Users/emeryj/hellbender/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/alleleSpecific/NA12892.AS.chr20snippet.g.vcf)])] out=/Users/emeryj/hellbender/gatk/gatk3results/4219bd4260e150949c234bd2b26369a9.vcf convertToBasePairResolution=false breakBandsAtMultiplesOf=0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
 ##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:39:50 EDT 2017",Epoch=1498567190652,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/Users/gauthier/workspaces/gsa-unstable/private/gatk-tools-private/src/test/resources//NA12878.HiSeq.b37.chr20.10_11mb.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genotypegvcf6825998583462616079.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.output.g.vcf --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR --annotation ClippingRankSumTest --annotation-group AS_StandardAnnotation --annotation-group StandardAnnotation --allow-old-rms-mapping-quality-annotation-data true  --include-non-variant-sites false --merge-input-intervals false --input-is-somatic false --tumor-lod-to-emit 3.5 --allele-fraction-error 0.001 --keep-combined-raw-annotations false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version="Unavailable",Date="August 2, 2019 3:58:41 PM EDT">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
 ##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
 ##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
 ##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient">
 ##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
 ##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
@@ -51,29 +51,28 @@
 ##contig=<ID=20,length=63025520,assembly=b37>
 ##contig=<ID=21,length=48129895,assembly=b37>
 ##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA12892
-20	10087820	.	C	CAGAGAG,CAG	892.52	.	AC=1,1;AF=0.250,0.250;AN=4;AS_BaseQRankSum=1.000,-2.100;AS_FS=0.000,2.538;AS_MQ=44.37,60.00;AS_MQRankSum=-3.100,0.600;AS_QD=6.80,3.82;AS_ReadPosRankSum=-0.300,-0.400;AS_SOR=0.634,1.096;BaseQRankSum=0.955;DP=167;ExcessHet=4.7712;FS=0.000;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.95;MQRankSum=0.678;QD=8.84;RAW_MQ=541599.00;ReadPosRankSum=-2.540e-01;SOR=0.728	GT:AD:GQ:PL	0/2:35,0,13:99:302,483,1922,0,1169,1079	0/1:29,24,0:99:606,0,849,697,927,1653
-20	10433322	.	A	AT	564.50	.	AC=2;AF=0.500;AN=4;AS_BaseQRankSum=1.650;AS_FS=0.000;AS_MQ=49.30;AS_MQRankSum=1.650;AS_QD=13.75;AS_ReadPosRankSum=1.950;AS_SOR=0.681;BaseQRankSum=2.56;DP=77;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=44.80;MQRankSum=1.90;QD=17.64;RAW_MQ=154528.00;ReadPosRankSum=2.04;SOR=0.582	GT:AD:GQ:PL	0/1:11,5:99:124,0,369	0/1:4,12:46:450,0,46
-20	10433324	.	A	T	1091.09	.	AC=3;AF=0.750;AN=4;AS_BaseQRankSum=2.200;AS_FS=6.118;AS_MQ=43.36;AS_MQRankSum=0.500;AS_QD=31.17;AS_ReadPosRankSum=1.500;AS_SOR=0.132;BaseQRankSum=2.28;DP=73;ExcessHet=3.0103;FS=6.118;MLEAC=3;MLEAF=0.750;MQ=43.81;MQRankSum=0.871;QD=31.17;RAW_MQ=140128.00;ReadPosRankSum=1.74;SOR=0.132	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275	1/1:1,20:53:1|1:10433324_A_T:877,53,0
-20	10433326	.	A	T	1091.09	.	AC=3;AF=0.750;AN=4;AS_BaseQRankSum=0.800;AS_FS=6.118;AS_MQ=43.36;AS_MQRankSum=0.500;AS_QD=31.17;AS_ReadPosRankSum=1.400;AS_SOR=0.132;BaseQRankSum=1.54;DP=67;ExcessHet=3.0103;FS=6.118;MLEAC=3;MLEAF=0.750;MQ=42.06;MQRankSum=0.871;QD=31.17;RAW_MQ=118528.00;ReadPosRankSum=1.74;SOR=0.132	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275	1/1:1,20:53:1|1:10433324_A_T:877,53,0
+20	10087820	.	C	CAGAGAG,CAG	892.45	.	AC=1,1;AF=0.250,0.250;AN=4;AS_BaseQRankSum=1.000,-2.100;AS_FS=0.000,2.538;AS_MQ=44.37,60.00;AS_MQRankSum=-3.100,0.600;AS_QD=6.80,3.82;AS_ReadPosRankSum=-0.300,-0.400;AS_SOR=0.634,1.096;BaseQRankSum=0.955;DP=167;ExcessHet=4.7712;FS=0.000;MLEAC=1,1;MLEAF=0.250,0.250;MQ=56.95;MQRankSum=0.678;QD=8.84;RAW_MQ=541599.00;ReadPosRankSum=-2.540e-01;SOR=0.728	GT:AD:GQ:PL	0/2:35,0,13:99:302,483,1922,0,1169,1079	0/1:29,24,0:99:606,0,849,697,927,1653
+20	10433322	.	A	AT	564.46	.	AC=2;AF=0.500;AN=4;AS_BaseQRankSum=1.650;AS_FS=0.000;AS_MQ=49.30;AS_MQRankSum=1.650;AS_QD=14.03;AS_ReadPosRankSum=1.950;AS_SOR=0.681;BaseQRankSum=2.56;DP=77;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=44.80;MQRankSum=1.90;QD=17.64;RAW_MQ=154528.00;ReadPosRankSum=2.04;SOR=0.582	GT:AD:GQ:PL	0/1:11,5:99:124,0,369	0/1:4,12:46:450,0,46
+20	10433324	.	A	T	1091.13	.	AC=3;AF=0.750;AN=4;AS_BaseQRankSum=2.200;AS_FS=6.118;AS_MQ=43.36;AS_MQRankSum=0.500;AS_QD=31.17;AS_ReadPosRankSum=1.500;AS_SOR=0.132;BaseQRankSum=2.28;DP=73;ExcessHet=3.0103;FS=6.118;MLEAC=3;MLEAF=0.750;MQ=43.81;MQRankSum=0.871;QD=31.18;RAW_MQ=140128.00;ReadPosRankSum=1.74;SOR=0.132	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275	1/1:1,20:53:1|1:10433324_A_T:877,53,0
+20	10433326	.	A	T	1091.13	.	AC=3;AF=0.750;AN=4;AS_BaseQRankSum=0.800;AS_FS=6.118;AS_MQ=43.36;AS_MQRankSum=0.500;AS_QD=31.17;AS_ReadPosRankSum=1.400;AS_SOR=0.132;BaseQRankSum=1.54;DP=67;ExcessHet=3.0103;FS=6.118;MLEAC=3;MLEAF=0.750;MQ=42.06;MQRankSum=0.871;QD=31.18;RAW_MQ=118528.00;ReadPosRankSum=1.74;SOR=0.132	GT:AD:GQ:PGT:PID:PL	0/1:8,6:99:0|1:10433324_A_T:228,0,275	1/1:1,20:53:1|1:10433324_A_T:877,53,0
 20	10433328	.	A	T,ATATAT	2087.37	.	AC=3,1;AF=0.750,0.250;AN=4;AS_BaseQRankSum=.,.;AS_FS=0.000,0.000;AS_MQ=43.36,29.00;AS_MQRankSum=.,.;AS_QD=25.36,28.73;AS_ReadPosRankSum=.,.;AS_SOR=0.693,1.179;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=41.73;QD=30.97;RAW_MQ=114928.00;SOR=0.760	GT:AD:GQ:PL	1/2:0,6,3:99:919,177,246,420,0,500	1/1:0,20,0:74:1191,74,0,1132,93,1376
-20	10433382	.	T	C	623.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.900;AS_FS=0.000;AS_MQ=55.21;AS_MQRankSum=1.000;AS_QD=20.80;AS_ReadPosRankSum=0.200;AS_SOR=0.998;BaseQRankSum=-1.821e+00;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=53.72;MQRankSum=1.03;QD=20.80;RAW_MQ=86585.00;ReadPosRankSum=0.249;SOR=0.998	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,15:.:99:0|1:10433382_T_C:632,0,601	0/0:36,0:36:99:.:.:0,99,1182
-20	10433391	.	T	C	622.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-0.300;AS_FS=0.000;AS_MQ=57.05;AS_MQRankSum=1.300;AS_QD=18.32;AS_ReadPosRankSum=1.500;AS_SOR=0.859;BaseQRankSum=-2.840e-01;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=55.24;MQRankSum=1.33;QD=18.32;RAW_MQ=103744.00;ReadPosRankSum=1.54;SOR=0.859	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:.:99:0|1:10433382_T_C:631,0,673	0/0:36,0:36:99:.:.:0,99,1182
-20	10433468	.	T	C	644.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.400;AS_FS=2.955;AS_MQ=58.84;AS_MQRankSum=0.000;AS_QD=16.97;AS_ReadPosRankSum=1.400;AS_SOR=0.324;BaseQRankSum=-1.312e+00;DP=68;ExcessHet=3.0103;FS=2.955;MLEAC=1;MLEAF=0.250;MQ=59.00;MQRankSum=0.076;QD=16.97;RAW_MQ=132290.00;ReadPosRankSum=1.46;SOR=0.324	GT:AD:DP:GQ:PL	0/1:18,20:.:99:653,0,572	0/0:30,0:30:81:0,81,1215
-20	10433560	.	C	A	986.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=3.400;AS_FS=5.027;AS_MQ=59.25;AS_MQRankSum=-1.100;AS_QD=17.63;AS_ReadPosRankSum=1.300;AS_SOR=0.129;BaseQRankSum=3.50;DP=95;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.250;MQ=59.67;MQRankSum=-1.078e+00;QD=17.62;RAW_MQ=199369.00;ReadPosRankSum=1.38;SOR=0.129	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,25:.:99:0|1:10433560_C_A:995,0,3032	0/0:39,0:39:99:.:.:0,99,1485
-20	10433575	.	C	T	1142.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=3.800;AS_FS=1.568;AS_MQ=57.81;AS_MQRankSum=-1.200;AS_QD=17.86;AS_ReadPosRankSum=0.800;AS_SOR=0.375;BaseQRankSum=3.81;DP=103;ExcessHet=3.0103;FS=1.568;MLEAC=1;MLEAF=0.250;MQ=58.62;MQRankSum=-1.123e+00;QD=17.86;RAW_MQ=219892.00;ReadPosRankSum=0.830;SOR=0.375	GT:AD:DP:GQ:PGT:PID:PL	0/1:34,30:.:99:0|1:10433560_C_A:1151,0,3385	0/0:39,0:39:99:.:.:0,99,1485
-20	10433594	.	C	T	1104.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=4.800;AS_FS=1.535;AS_MQ=54.33;AS_MQRankSum=-2.400;AS_QD=18.42;AS_ReadPosRankSum=-0.600;AS_SOR=0.415;BaseQRankSum=4.82;DP=100;ExcessHet=3.0103;FS=1.535;MLEAC=1;MLEAF=0.250;MQ=56.66;MQRankSum=-2.334e+00;QD=18.41;RAW_MQ=195825.00;ReadPosRankSum=-5.020e-01;SOR=0.415	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,29:.:99:0|1:10433560_C_A:1113,0,3070	0/0:39,0:39:99:.:.:0,99,1485
-20	10433809	.	A	G	1134.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=1.400;AS_FS=0.968;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=17.20;AS_ReadPosRankSum=-0.500;AS_SOR=0.930;BaseQRankSum=1.41;DP=105;ExcessHet=3.0103;FS=0.968;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=0.00;QD=17.20;RAW_MQ=242569.00;ReadPosRankSum=-4.450e-01;SOR=0.930	GT:AD:DP:GQ:PL	0/1:32,34:.:99:1143,0,1041	0/0:37,0:37:99:0,99,1485
-20	10433955	.	C	CGTGTGTGTGTAT	1026.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_MQ=40.57;AS_MQRankSum=-4.000;AS_QD=24.45;AS_ReadPosRankSum=-0.800;AS_SOR=0.710;BaseQRankSum=0.422;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=49.96;MQRankSum=-4.001e+00;QD=24.45;RAW_MQ=117307.00;ReadPosRankSum=-7.890e-01;SOR=0.710	GT:AD:DP:GQ:PL	0/1:18,24:.:99:1035,0,1217	0/0:37,0:37:99:0,99,1485
-20	10434177	.	A	T	1466.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=0.900;AS_FS=0.888;AS_MQ=55.78;AS_MQRankSum=-2.500;AS_QD=20.10;AS_ReadPosRankSum=-0.900;AS_SOR=0.836;BaseQRankSum=0.903;DP=111;ExcessHet=3.0103;FS=0.888;MLEAC=1;MLEAF=0.250;MQ=57.58;MQRankSum=-2.473e+00;QD=20.09;RAW_MQ=245384.00;ReadPosRankSum=-8.910e-01;SOR=0.836	GT:AD:DP:GQ:PL	0/1:30,43:.:99:1475,0,936	0/0:37,0:37:99:0,102,1530
-20	10434258	.	G	A	1234.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=3.000;AS_FS=0.000;AS_MQ=52.93;AS_MQRankSum=-2.900;AS_QD=17.90;AS_ReadPosRankSum=-0.200;AS_SOR=0.776;BaseQRankSum=3.06;DP=107;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=55.99;MQRankSum=-2.871e+00;QD=17.90;RAW_MQ=219420.00;ReadPosRankSum=-1.550e-01;SOR=0.776	GT:AD:DP:GQ:PL	0/1:31,38:.:99:1243,0,1003	0/0:37,0:37:99:0,102,1530
+20	10433382	.	T	C	623.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.900;AS_FS=0.000;AS_MQ=55.21;AS_MQRankSum=1.000;AS_QD=20.80;AS_ReadPosRankSum=0.200;AS_SOR=0.998;BaseQRankSum=-1.821e+00;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=53.72;MQRankSum=1.03;QD=20.80;RAW_MQ=86585.00;ReadPosRankSum=0.249;SOR=0.998	GT:AD:DP:GQ:PGT:PID:PL	0/1:15,15:.:99:0|1:10433382_T_C:632,0,601	0/0:36,0:36:99:.:.:0,99,1182
+20	10433391	.	T	C	622.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-0.300;AS_FS=0.000;AS_MQ=57.05;AS_MQRankSum=1.300;AS_QD=18.32;AS_ReadPosRankSum=1.500;AS_SOR=0.859;BaseQRankSum=-2.840e-01;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=55.24;MQRankSum=1.33;QD=18.32;RAW_MQ=103744.00;ReadPosRankSum=1.54;SOR=0.859	GT:AD:DP:GQ:PGT:PID:PL	0/1:18,16:.:99:0|1:10433382_T_C:631,0,673	0/0:36,0:36:99:.:.:0,99,1182
+20	10433468	.	T	C	644.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.400;AS_FS=2.955;AS_MQ=58.84;AS_MQRankSum=0.000;AS_QD=16.97;AS_ReadPosRankSum=1.400;AS_SOR=0.324;BaseQRankSum=-1.312e+00;DP=68;ExcessHet=3.0103;FS=2.955;MLEAC=1;MLEAF=0.250;MQ=59.00;MQRankSum=0.076;QD=16.97;RAW_MQ=132290.00;ReadPosRankSum=1.46;SOR=0.324	GT:AD:DP:GQ:PL	0/1:18,20:.:99:653,0,572	0/0:30,0:30:81:0,81,1215
+20	10433560	.	C	A	986.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=3.400;AS_FS=5.027;AS_MQ=59.25;AS_MQRankSum=-1.100;AS_QD=17.63;AS_ReadPosRankSum=1.300;AS_SOR=0.129;BaseQRankSum=3.50;DP=95;ExcessHet=3.0103;FS=5.027;MLEAC=1;MLEAF=0.250;MQ=59.67;MQRankSum=-1.078e+00;QD=17.62;RAW_MQ=199369.00;ReadPosRankSum=1.38;SOR=0.129	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,25:.:99:0|1:10433560_C_A:995,0,3032	0/0:39,0:39:99:.:.:0,99,1485
+20	10433575	.	C	T	1142.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=3.800;AS_FS=1.568;AS_MQ=57.81;AS_MQRankSum=-1.200;AS_QD=17.86;AS_ReadPosRankSum=0.800;AS_SOR=0.375;BaseQRankSum=3.81;DP=103;ExcessHet=3.0103;FS=1.568;MLEAC=1;MLEAF=0.250;MQ=58.62;MQRankSum=-1.123e+00;QD=17.86;RAW_MQ=219892.00;ReadPosRankSum=0.830;SOR=0.375	GT:AD:DP:GQ:PGT:PID:PL	0/1:34,30:.:99:0|1:10433560_C_A:1151,0,3385	0/0:39,0:39:99:.:.:0,99,1485
+20	10433594	.	C	T	1104.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=4.800;AS_FS=1.535;AS_MQ=54.33;AS_MQRankSum=-2.400;AS_QD=18.42;AS_ReadPosRankSum=-0.600;AS_SOR=0.415;BaseQRankSum=4.82;DP=100;ExcessHet=3.0103;FS=1.535;MLEAC=1;MLEAF=0.250;MQ=56.66;MQRankSum=-2.334e+00;QD=18.42;RAW_MQ=195825.00;ReadPosRankSum=-5.020e-01;SOR=0.415	GT:AD:DP:GQ:PGT:PID:PL	0/1:31,29:.:99:0|1:10433560_C_A:1113,0,3070	0/0:39,0:39:99:.:.:0,99,1485
+20	10433809	.	A	G	1134.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=1.400;AS_FS=0.968;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=17.20;AS_ReadPosRankSum=-0.500;AS_SOR=0.930;BaseQRankSum=1.41;DP=105;ExcessHet=3.0103;FS=0.968;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=0.00;QD=17.20;RAW_MQ=242569.00;ReadPosRankSum=-4.450e-01;SOR=0.930	GT:AD:DP:GQ:PL	0/1:32,34:.:99:1143,0,1041	0/0:37,0:37:99:0,99,1485
+20	10433955	.	C	CGTGTGTGTGTAT	1026.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_MQ=40.57;AS_MQRankSum=-4.000;AS_QD=24.45;AS_ReadPosRankSum=-0.800;AS_SOR=0.710;BaseQRankSum=0.422;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=49.96;MQRankSum=-4.001e+00;QD=24.45;RAW_MQ=117307.00;ReadPosRankSum=-7.890e-01;SOR=0.710	GT:AD:DP:GQ:PL	0/1:18,24:.:99:1035,0,1217	0/0:37,0:37:99:0,99,1485
+20	10434177	.	A	T	1466.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=0.900;AS_FS=0.888;AS_MQ=55.78;AS_MQRankSum=-2.500;AS_QD=20.10;AS_ReadPosRankSum=-0.900;AS_SOR=0.836;BaseQRankSum=0.903;DP=111;ExcessHet=3.0103;FS=0.888;MLEAC=1;MLEAF=0.250;MQ=57.58;MQRankSum=-2.473e+00;QD=20.09;RAW_MQ=245384.00;ReadPosRankSum=-8.910e-01;SOR=0.836	GT:AD:DP:GQ:PL	0/1:30,43:.:99:1475,0,936	0/0:37,0:37:99:0,102,1530
+20	10434258	.	G	A	1234.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=3.000;AS_FS=0.000;AS_MQ=52.93;AS_MQRankSum=-2.900;AS_QD=17.90;AS_ReadPosRankSum=-0.200;AS_SOR=0.776;BaseQRankSum=3.06;DP=107;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=55.99;MQRankSum=-2.871e+00;QD=17.90;RAW_MQ=219420.00;ReadPosRankSum=-1.550e-01;SOR=0.776	GT:AD:DP:GQ:PL	0/1:31,38:.:99:1243,0,1003	0/0:37,0:37:99:0,102,1530
 20	10434384	.	TA	T	781.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-0.100;AS_FS=0.000;AS_MQ=60.00;AS_MQRankSum=1.000;AS_QD=11.50;AS_ReadPosRankSum=0.400;AS_SOR=0.723;BaseQRankSum=-1.000e-01;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.74;MQRankSum=1.00;QD=11.50;RAW_MQ=253369.00;ReadPosRankSum=0.497;SOR=0.723	GT:AD:DP:GQ:PL	0/1:35,33:.:99:790,0,846	0/0:37,0:37:99:0,102,1530
-20	10434519	.	T	C	1463.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-3.200;AS_FS=1.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.77;AS_ReadPosRankSum=-0.800;AS_SOR=0.900;BaseQRankSum=-3.137e+00;DP=115;ExcessHet=3.0103;FS=1.877;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=18.77;RAW_MQ=280800.00;ReadPosRankSum=-7.490e-01;SOR=0.900	GT:AD:DP:GQ:PL	0/1:35,43:.:99:1472,0,1192	0/0:37,0:37:99:0,102,1530
+20	10434519	.	T	C	1463.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-3.200;AS_FS=1.877;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=18.77;AS_ReadPosRankSum=-0.800;AS_SOR=0.900;BaseQRankSum=-3.137e+00;DP=115;ExcessHet=3.0103;FS=1.877;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=18.77;RAW_MQ=280800.00;ReadPosRankSum=-7.490e-01;SOR=0.900	GT:AD:DP:GQ:PL	0/1:35,43:.:99:1472,0,1192	0/0:37,0:37:99:0,102,1530
 20	10435067	.	GTA	G	1445.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=2.600;AS_FS=3.289;AS_MQ=60.00;AS_MQRankSum=0.000;AS_QD=21.58;AS_ReadPosRankSum=-0.200;AS_SOR=1.121;BaseQRankSum=2.60;DP=104;ExcessHet=3.0103;FS=3.289;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=21.58;RAW_MQ=241200.00;ReadPosRankSum=-1.830e-01;SOR=1.121	GT:AD:DP:GQ:PL	0/1:30,37:.:99:1454,0,1191	0/0:37,0:37:99:0,102,1530
-20	10435948	.	A	C	1136.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-4.700;AS_FS=3.002;AS_MQ=54.65;AS_MQRankSum=-3.200;AS_QD=14.96;AS_ReadPosRankSum=-1.600;AS_SOR=0.855;BaseQRankSum=-4.692e+00;DP=113;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.250;MQ=57.53;MQRankSum=-3.121e+00;QD=14.96;RAW_MQ=251528.00;ReadPosRankSum=-1.594e+00;SOR=0.855	GT:AD:DP:GQ:PL	0/1:40,36:.:99:1145,0,1413	0/0:37,0:37:99:0,102,1530
-20	10436227	.	TTTTATTTATTTATTTATTTA	TTTTATTTATTTATTTATTTATTTA,T	1627.36	.	AC=3,1;AF=0.750,0.250;AN=4;AS_BaseQRankSum=.,.;AS_FS=0.000,0.000;AS_MQ=53.62,32.72;AS_MQRankSum=.,.;AS_QD=27.24,28.20;AS_ReadPosRankSum=.,.;AS_SOR=0.551,0.382;BaseQRankSum=-1.450e+00;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=53.84;MQRankSum=-1.660e+00;QD=25.00;RAW_MQ=313019.00;ReadPosRankSum=1.30;SOR=0.460	GT:AD:GQ:PL	1/2:1,7,24:99:1225,947,970,241,0,589	1/1:0,10,0:29:425,29,0,427,30,428
-20	10436415	.	A	G	1189.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-2.800;AS_FS=9.312;AS_MQ=59.42;AS_MQRankSum=0.400;AS_QD=18.89;AS_ReadPosRankSum=-0.100;AS_SOR=0.739;BaseQRankSum=-2.775e+00;DP=97;ExcessHet=3.0103;FS=9.312;MLEAC=1;MLEAF=0.250;MQ=59.51;MQRankSum=0.399;QD=18.89;RAW_MQ=223145.00;ReadPosRankSum=-6.300e-02;SOR=0.739	GT:AD:DP:GQ:PL	0/1:23,40:.:99:1198,0,691	0/0:34,0:34:99:0,99,1485
-20	10436582	.	A	G	1186.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.400;AS_FS=3.189;AS_MQ=52.86;AS_MQRankSum=-2.700;AS_QD=16.72;AS_ReadPosRankSum=0.200;AS_SOR=0.906;BaseQRankSum=-1.326e+00;DP=105;ExcessHet=3.0103;FS=3.189;MLEAC=1;MLEAF=0.250;MQ=55.76;MQRankSum=-2.639e+00;QD=16.72;RAW_MQ=220789.00;ReadPosRankSum=0.267;SOR=0.906	GT:AD:DP:GQ:PL	0/1:34,37:.:99:1195,0,1113	0/0:34,0:34:99:0,99,1485
-20	10436700	.	A	G	1332.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.400;AS_FS=2.012;AS_MQ=59.53;AS_MQRankSum=-0.900;AS_QD=19.04;AS_ReadPosRankSum=0.500;AS_SOR=0.449;BaseQRankSum=-1.329e+00;DP=104;ExcessHet=3.0103;FS=2.012;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=-8.370e-01;QD=19.04;RAW_MQ=249769.00;ReadPosRankSum=0.581;SOR=0.449	GT:AD:DP:GQ:PL	0/1:30,40:.:99:1341,0,961	0/0:34,0:34:99:0,99,1485
-20	10436908	.	C	G	1360.88	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-0.900;AS_FS=4.557;AS_MQ=58.89;AS_MQRankSum=-1.000;AS_QD=16.40;AS_ReadPosRankSum=-0.200;AS_SOR=1.252;BaseQRankSum=-8.440e-01;DP=117;ExcessHet=3.0103;FS=4.557;MLEAC=1;MLEAF=0.250;MQ=59.26;MQRankSum=-9.940e-01;QD=16.40;RAW_MQ=291487.00;ReadPosRankSum=-1.480e-01;SOR=1.252	GT:AD:DP:GQ:PL	0/1:41,42:.:99:1369,0,1378	0/0:34,0:34:99:0,99,1485
+20	10435948	.	A	C	1136.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-4.700;AS_FS=3.002;AS_MQ=54.65;AS_MQRankSum=-3.200;AS_QD=14.96;AS_ReadPosRankSum=-1.600;AS_SOR=0.855;BaseQRankSum=-4.692e+00;DP=113;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.250;MQ=57.53;MQRankSum=-3.121e+00;QD=14.96;RAW_MQ=251528.00;ReadPosRankSum=-1.594e+00;SOR=0.855	GT:AD:DP:GQ:PL	0/1:40,36:.:99:1145,0,1413	0/0:37,0:37:99:0,102,1530
+20	10436227	.	TTTTATTTATTTATTTATTTA	TTTTATTTATTTATTTATTTATTTA,T	1627.32	.	AC=3,1;AF=0.750,0.250;AN=4;AS_BaseQRankSum=.,.;AS_FS=0.000,0.000;AS_MQ=53.62,32.72;AS_MQRankSum=.,.;AS_QD=27.24,28.20;AS_ReadPosRankSum=.,.;AS_SOR=0.551,0.382;BaseQRankSum=-1.450e+00;DP=108;ExcessHet=3.0103;FS=0.000;MLEAC=3,1;MLEAF=0.750,0.250;MQ=53.84;MQRankSum=-1.660e+00;QD=25.00;RAW_MQ=313019.00;ReadPosRankSum=1.30;SOR=0.460	GT:AD:GQ:PL	1/2:1,7,24:99:1225,947,970,241,0,589	1/1:0,10,0:29:425,29,0,427,30,428
+20	10436415	.	A	G	1189.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-2.800;AS_FS=9.312;AS_MQ=59.42;AS_MQRankSum=0.400;AS_QD=18.89;AS_ReadPosRankSum=-0.100;AS_SOR=0.739;BaseQRankSum=-2.775e+00;DP=97;ExcessHet=3.0103;FS=9.312;MLEAC=1;MLEAF=0.250;MQ=59.51;MQRankSum=0.399;QD=18.89;RAW_MQ=223145.00;ReadPosRankSum=-6.300e-02;SOR=0.739	GT:AD:DP:GQ:PL	0/1:23,40:.:99:1198,0,691	0/0:34,0:34:99:0,99,1485
+20	10436582	.	A	G	1186.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.400;AS_FS=3.189;AS_MQ=52.86;AS_MQRankSum=-2.700;AS_QD=16.72;AS_ReadPosRankSum=0.200;AS_SOR=0.906;BaseQRankSum=-1.326e+00;DP=105;ExcessHet=3.0103;FS=3.189;MLEAC=1;MLEAF=0.250;MQ=55.76;MQRankSum=-2.639e+00;QD=16.72;RAW_MQ=220789.00;ReadPosRankSum=0.267;SOR=0.906	GT:AD:DP:GQ:PL	0/1:34,37:.:99:1195,0,1113	0/0:34,0:34:99:0,99,1485
+20	10436700	.	A	G	1332.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-1.400;AS_FS=2.012;AS_MQ=59.53;AS_MQRankSum=-0.900;AS_QD=19.04;AS_ReadPosRankSum=0.500;AS_SOR=0.449;BaseQRankSum=-1.329e+00;DP=104;ExcessHet=3.0103;FS=2.012;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=-8.370e-01;QD=19.04;RAW_MQ=249769.00;ReadPosRankSum=0.581;SOR=0.449	GT:AD:DP:GQ:PL	0/1:30,40:.:99:1341,0,961	0/0:34,0:34:99:0,99,1485
+20	10436908	.	C	G	1360.91	.	AC=1;AF=0.250;AN=4;AS_BaseQRankSum=-0.900;AS_FS=4.557;AS_MQ=58.89;AS_MQRankSum=-1.000;AS_QD=16.40;AS_ReadPosRankSum=-0.200;AS_SOR=1.252;BaseQRankSum=-8.440e-01;DP=117;ExcessHet=3.0103;FS=4.557;MLEAC=1;MLEAF=0.250;MQ=59.26;MQRankSum=-9.940e-01;QD=16.40;RAW_MQ=291487.00;ReadPosRankSum=-1.480e-01;SOR=1.252	GT:AD:DP:GQ:PL	0/1:41,42:.:99:1369,0,1378	0/0:34,0:34:99:0,99,1485
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.expected.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testAlleleSpecificAnnotations.CombineGVCF.expected.g.vcf.idx
index 800c9cf152afead328503c7cd65b625793f537bc..3428437b829fb4aa5d2f3a1fc29fd1d30caffc41 100644
GIT binary patch
delta 289
zcmb`AO%4G;5QT{gSUAVjj<pbCDZ<J^PtP+tT9<Uy_*uCEmv9(6H*f+6urfy6z}r;v
z^40gQjaTE`I!y&p$nID0CQzSku|d$X;S7`;U6Vvh3Q>v>E~14H$DGp0CUZg5X`!I<
z-=_!}A}O;M+8e+AsD}uw$1R4l-asl**L!$Owy<v5cD5Tzz^LOONsl+F3l*E-P!ftP
f$&;O3*6Q<GmD_0i&`WV&G~3_eU-#Mh`hG)i^;Arm

delta 204
zcmeyxyo`B*NMc!Hk$zf!PD*M~v3{AUetJ@No@q{*rD?LMVRn{rML~sWK~-LIadKWo
zT70g4h<<u%UVcesL27zga+;Zik*TGng{g(HiJ6g^p_zfXr5;e2p(dFD3^KO949=N&
T@?t`_EkuA?bf!JTJeWlQw$m;E

diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf
index 2864b2624fd..ebaaa69d9ff 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf
@@ -11,7 +11,6 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs  --output /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf --variant /Users/davidben/broad/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/testUpdatePGT.gvcf --reference /Users/davidben/broad/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --include-non-variant-sites false --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=Unavailable,Date="January 27, 2019 1:19:14 AM EST">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -117,78 +116,77 @@
 ##contig=<ID=GL000225.1,length=211173,assembly=b37>
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
-##source=GenotypeGVCFs
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	.	C	T	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.440;DP=40;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.378e+00;QD=16.67;ReadPosRankSum=-1.262e+00;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
-20	10000211	.	C	T	659.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.995;ClippingRankSum=1.45;DP=45;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.84;MQ0=0;MQRankSum=-2.455e+00;QD=15.70;ReadPosRankSum=1.32;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
-20	10000439	.	T	G	1757.03	.	AC=2;AF=1.00;AN=2;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.33;MQ0=0;QD=31.38;SOR=1.412	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
-20	10000598	.	T	A	1774.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.33;MQ0=0;QD=33.47;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
-20	10000694	.	G	A	982.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.900;ClippingRankSum=-6.640e-01;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.518;QD=18.54;ReadPosRankSum=0.991;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
-20	10000758	.	T	A	1682.03	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;QD=33.64;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1696,149,0
-20	10001019	.	T	G	114.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.347;ClippingRankSum=-6.940e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.34;MQ0=0;MQRankSum=-5.780e-01;QD=4.41;ReadPosRankSum=-4.620e-01;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
-20	10001298	.	T	A	1424.03	.	AC=2;AF=1.00;AN=2;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=169.60;MQ0=0;QD=34.73;SOR=0.954	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
-20	10001436	.	A	AAGGCT	1876.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=1.005	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1890,126,0
-20	10001474	.	C	T	1614.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;QD=28.73;SOR=1.055	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
-20	10001617	.	C	A	633.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.400e-02;ClippingRankSum=0.192;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.404e+00;QD=16.67;ReadPosRankSum=0.251;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
-20	10001628	.	G	A	1387.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;QD=30.97;SOR=1.096	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
-20	10001661	.	T	C	1514.03	.	AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.44;MQ0=0;QD=27.24;SOR=1.148	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,35:35:99:1|1:10001661_T_C:1528,105,0
-20	10001670	.	T	G	1426.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.70;MQ0=0;QD=28.20;SOR=1.112	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,32:32:96:1|1:10001661_T_C:1440,96,0
-20	10002058	.	T	G	1722.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.79;MQ0=0;QD=25.00;SOR=0.909	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
-20	10002099	.	C	T	614.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.370e-01;ClippingRankSum=-6.120e-01;DP=55;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.15;MQ0=0;MQRankSum=-1.893e+00;QD=12.29;ReadPosRankSum=1.72;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
-20	10002138	.	C	G	2143.03	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.87;MQ0=0;QD=29.56;SOR=0.818	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,49:49:99:1|1:10002138_C_G:2157,147,0
-20	10002142	.	G	C	2134.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.64;MQ0=0;QD=30.62;SOR=0.735	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,47:47:99:1|1:10002138_C_G:2148,144,0
-20	10002458	.	G	GTT,GTTT	1096.10	.	AC=1,1;AF=0.500,0.500;AN=2;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=188.54;MQ0=0;QD=28.17;SOR=3.912	GT:AD:DP:GQ:PL	1/2:0,8,6:14:84:1113,165,84,188,0,107
-20	10002470	.	C	T	1209.03	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=180.88;MQ0=0;QD=26.80;SOR=0.906	GT:AD:DP:GQ:PL	1/1:0,29:29:87:1223,87,0
-20	10002625	.	G	T	1339.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;QD=34.33;SOR=0.743	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
-20	10003021	.	C	T	1393.03	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.10;MQ0=0;QD=34.83;SOR=0.793	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
-20	10003358	.	A	C	377.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;ClippingRankSum=-5.700e-02;DP=34;ExcessHet=3.0103;FS=3.270;MLEAC=1;MLEAF=0.500;MQ=225.04;MQ0=0;MQRankSum=-8.170e-01;QD=11.80;ReadPosRankSum=-7.410e-01;SOR=1.445	GT:AD:DP:GQ:PL	0/1:18,14:32:99:385,0,503
-20	10003651	.	T	C	1401.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;QD=26.00;SOR=1.151	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
-20	10003692	.	A	G	1602.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.61;MQ0=0;QD=34.09;SOR=0.823	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1616,141,0
-20	10003832	.	G	A	1872.03	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.21;MQ0=0;QD=34.04;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,55:55:99:1886,165,0
-20	10004094	.	A	C	943.03	.	AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=101.97;MQ0=0;QD=31.43;SOR=2.019	GT:AD:DP:GQ:PL	1/1:0,30:30:90:957,90,0
-20	10004147	.	A	G	557.03	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;QD=24.22;SOR=1.708	GT:AD:DP:GQ:PL	1/1:0,23:23:66:571,66,0
-20	10004193	.	G	T	294.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.260e-01;ClippingRankSum=0.253;DP=22;ExcessHet=3.0103;FS=8.351;MLEAC=1;MLEAF=0.500;MQ=102.21;MQ0=0;MQRankSum=0.833;QD=14.03;ReadPosRankSum=-1.340e+00;SOR=2.833	GT:AD:DP:GQ:PL	0/1:8,13:21:99:302,0,223
-20	10004222	.	C	CA	184.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.460e-01;ClippingRankSum=0.178;DP=26;ExcessHet=3.0103;FS=7.991;MLEAC=1;MLEAF=0.500;MQ=136.85;MQ0=0;MQRankSum=-6.040e-01;QD=8.79;ReadPosRankSum=0.462;SOR=0.415	GT:AD:DP:GQ:PL	0/1:12,9:21:99:192,0,328
-20	10004223	.	A	AG	268.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;ClippingRankSum=-6.290e-01;DP=32;ExcessHet=3.0103;FS=14.989;MLEAC=1;MLEAF=0.500;MQ=150.36;MQ0=0;MQRankSum=0.304;QD=8.67;ReadPosRankSum=1.28;SOR=2.640	GT:AD:DP:GQ:PL	0/1:19,12:31:99:276,0,464
-20	10004351	.	C	G	1638.03	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.57;MQ0=0;QD=30.02;SOR=0.784	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1652,132,0
-20	10004389	.	T	G	1895.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;QD=31.98;SOR=0.770	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1909,156,0
-20	10004610	.	A	C	1600.03	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.18;MQ0=0;QD=32.65;SOR=1.112	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1614,146,0
-20	10004725	.	A	G	602.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.22;ClippingRankSum=-1.380e-01;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=216.57;MQ0=0;MQRankSum=1.95;QD=12.82;ReadPosRankSum=0.543;SOR=0.784	GT:AD:DP:GQ:PL	0/1:24,23:47:99:610,0,600
+20	10000117	.	C	T	633.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.440;DP=40;ExcessHet=3.0103;FS=4.666;MLEAC=1;MLEAF=0.500;MQ=221.39;MQ0=0;MQRankSum=-2.378e+00;QD=16.67;ReadPosRankSum=-1.262e+00;SOR=0.426	GT:AD:DP:GQ:PL	0/1:17,21:38:99:641,0,456
+20	10000211	.	C	T	659.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.995;ClippingRankSum=1.45;DP=45;ExcessHet=3.0103;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=221.84;MQ0=0;MQRankSum=-2.455e+00;QD=15.71;ReadPosRankSum=1.32;SOR=0.738	GT:AD:DP:GQ:PL	0/1:20,22:42:99:667,0,566
+20	10000439	.	T	G	1757.06	.	AC=2;AF=1.00;AN=2;DP=58;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.33;MQ0=0;QD=31.38;SOR=1.412	GT:AD:DP:GQ:PL	1/1:0,56:56:99:1771,168,0
+20	10000598	.	T	A	1774.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=185.33;MQ0=0;QD=33.47;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,53:53:99:1788,158,0
+20	10000694	.	G	A	982.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.900;ClippingRankSum=-6.640e-01;DP=54;ExcessHet=3.0103;FS=2.527;MLEAC=1;MLEAF=0.500;MQ=106.92;MQ0=0;MQRankSum=0.518;QD=18.54;ReadPosRankSum=0.991;SOR=1.277	GT:AD:DP:GQ:PL	0/1:21,32:53:99:990,0,579
+20	10000758	.	T	A	1682.06	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.32;MQ0=0;QD=33.64;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1696,149,0
+20	10001019	.	T	G	114.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.347;ClippingRankSum=-6.940e-01;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.34;MQ0=0;MQRankSum=-5.780e-01;QD=4.41;ReadPosRankSum=-4.620e-01;SOR=0.465	GT:AD:DP:GQ:PL	0/1:19,7:26:99:122,0,494
+20	10001298	.	T	A	1424.06	.	AC=2;AF=1.00;AN=2;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=169.60;MQ0=0;QD=34.73;SOR=0.954	GT:AD:DP:GQ:PL	1/1:0,41:41:99:1438,123,0
+20	10001436	.	A	AAGGCT	1876.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=1.005	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1890,126,0
+20	10001474	.	C	T	1614.06	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.09;MQ0=0;QD=28.73;SOR=1.055	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1628,129,0
+20	10001617	.	C	A	633.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.400e-02;ClippingRankSum=0.192;DP=38;ExcessHet=3.0103;FS=2.913;MLEAC=1;MLEAF=0.500;MQ=218.91;MQ0=0;MQRankSum=-1.404e+00;QD=16.67;ReadPosRankSum=0.251;SOR=1.329	GT:AD:DP:GQ:PL	0/1:16,22:38:99:641,0,435
+20	10001628	.	G	A	1387.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.15;MQ0=0;QD=30.97;SOR=1.096	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1401,117,0
+20	10001661	.	T	C	1514.06	.	AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.44;MQ0=0;QD=27.24;SOR=1.148	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,35:35:99:1|1:10001661_T_C:1528,105,0
+20	10001670	.	T	G	1426.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.70;MQ0=0;QD=28.20;SOR=1.112	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,32:32:96:1|1:10001661_T_C:1440,96,0
+20	10002058	.	T	G	1722.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.79;MQ0=0;QD=25.00;SOR=0.909	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1736,147,0
+20	10002099	.	C	T	614.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.370e-01;ClippingRankSum=-6.120e-01;DP=55;ExcessHet=3.0103;FS=5.900;MLEAC=1;MLEAF=0.500;MQ=219.15;MQ0=0;MQRankSum=-1.893e+00;QD=12.29;ReadPosRankSum=1.72;SOR=0.823	GT:AD:DP:GQ:PL	0/1:26,24:50:99:622,0,686
+20	10002138	.	C	G	2143.06	.	AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.87;MQ0=0;QD=29.56;SOR=0.818	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,49:49:99:1|1:10002138_C_G:2157,147,0
+20	10002142	.	G	C	2134.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.64;MQ0=0;QD=30.62;SOR=0.735	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,47:47:99:1|1:10002138_C_G:2148,144,0
+20	10002458	.	G	GTT,GTTT	1096.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=188.54;MQ0=0;QD=28.17;SOR=3.912	GT:AD:DP:GQ:PL	1/2:0,8,6:14:84:1113,165,84,188,0,107
+20	10002470	.	C	T	1209.06	.	AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=180.88;MQ0=0;QD=26.80;SOR=0.906	GT:AD:DP:GQ:PL	1/1:0,29:29:87:1223,87,0
+20	10002625	.	G	T	1339.06	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=213.41;MQ0=0;QD=34.33;SOR=0.743	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1353,116,0
+20	10003021	.	C	T	1393.06	.	AC=2;AF=1.00;AN=2;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.10;MQ0=0;QD=34.83;SOR=0.793	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1407,119,0
+20	10003358	.	A	C	377.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;ClippingRankSum=-5.700e-02;DP=34;ExcessHet=3.0103;FS=3.270;MLEAC=1;MLEAF=0.500;MQ=225.04;MQ0=0;MQRankSum=-8.170e-01;QD=11.80;ReadPosRankSum=-7.410e-01;SOR=1.445	GT:AD:DP:GQ:PL	0/1:18,14:32:99:385,0,503
+20	10003651	.	T	C	1401.06	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=217.41;MQ0=0;QD=26.00;SOR=1.151	GT:AD:DP:GQ:PL	1/1:0,40:40:99:1415,120,0
+20	10003692	.	A	G	1602.06	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.61;MQ0=0;QD=34.09;SOR=0.823	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1616,141,0
+20	10003832	.	G	A	1872.06	.	AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.21;MQ0=0;QD=34.04;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,55:55:99:1886,165,0
+20	10004094	.	A	C	943.06	.	AC=2;AF=1.00;AN=2;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=101.97;MQ0=0;QD=31.44;SOR=2.019	GT:AD:DP:GQ:PL	1/1:0,30:30:90:957,90,0
+20	10004147	.	A	G	557.06	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=78.67;MQ0=0;QD=24.22;SOR=1.708	GT:AD:DP:GQ:PL	1/1:0,23:23:66:571,66,0
+20	10004193	.	G	T	294.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.260e-01;ClippingRankSum=0.253;DP=22;ExcessHet=3.0103;FS=8.351;MLEAC=1;MLEAF=0.500;MQ=102.21;MQ0=0;MQRankSum=0.833;QD=14.03;ReadPosRankSum=-1.340e+00;SOR=2.833	GT:AD:DP:GQ:PL	0/1:8,13:21:99:302,0,223
+20	10004222	.	C	CA	184.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.460e-01;ClippingRankSum=0.178;DP=26;ExcessHet=3.0103;FS=7.991;MLEAC=1;MLEAF=0.500;MQ=136.85;MQ0=0;MQRankSum=-6.040e-01;QD=8.79;ReadPosRankSum=0.462;SOR=0.415	GT:AD:DP:GQ:PL	0/1:12,9:21:99:192,0,328
+20	10004223	.	A	AG	268.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;ClippingRankSum=-6.290e-01;DP=32;ExcessHet=3.0103;FS=14.989;MLEAC=1;MLEAF=0.500;MQ=150.36;MQ0=0;MQRankSum=0.304;QD=8.66;ReadPosRankSum=1.28;SOR=2.640	GT:AD:DP:GQ:PL	0/1:19,12:31:99:276,0,464
+20	10004351	.	C	G	1638.06	.	AC=2;AF=1.00;AN=2;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.57;MQ0=0;QD=30.02;SOR=0.784	GT:AD:DP:GQ:PL	1/1:0,44:44:99:1652,132,0
+20	10004389	.	T	G	1895.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.26;MQ0=0;QD=31.98;SOR=0.770	GT:AD:DP:GQ:PL	1/1:0,52:52:99:1909,156,0
+20	10004610	.	A	C	1600.06	.	AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.18;MQ0=0;QD=32.65;SOR=1.112	GT:AD:DP:GQ:PL	1/1:0,49:49:99:1614,146,0
+20	10004725	.	A	G	602.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.22;ClippingRankSum=-1.380e-01;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=216.57;MQ0=0;MQRankSum=1.95;QD=12.82;ReadPosRankSum=0.543;SOR=0.784	GT:AD:DP:GQ:PL	0/1:24,23:47:99:610,0,600
 20	10004769	.	TAAAACTATGC	T	670.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.062e+00;ClippingRankSum=-1.874e+00;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=218.95;MQ0=0;MQRankSum=-4.022e+00;QD=15.24;ReadPosRankSum=0.557;SOR=0.752	GT:AD:DP:GQ:PL	0/1:26,18:44:99:678,0,1034
-20	10004874	.	A	C	1898.03	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.87;MQ0=0;QD=27.51;SOR=0.859	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,50:50:99:1|1:10004874_A_C:1912,150,0
-20	10004887	.	A	G	579.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.140;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=219.74;MQ0=0;MQRankSum=-3.798e+00;QD=12.33;ReadPosRankSum=1.26;SOR=0.813	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,20:47:99:0|1:10004874_A_C:587,0,795
-20	10005010	.	C	T	1376.03	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=223.84;MQ0=0;QD=29.11;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
-20	10005427	.	C	T	1839.03	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;QD=34.06;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
-20	10005499	.	A	G	1797.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=0.832;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.05;QD=32.67;ReadPosRankSum=1.82;SOR=0.730	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1811,116,0
-20	10005587	.	A	G	821.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.474;ClippingRankSum=0.831;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-3.660e-01;QD=15.50;ReadPosRankSum=-1.671e+00;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
-20	10005723	.	A	G	1461.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;QD=31.09;SOR=1.132	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
-20	10006291	.	G	A	456.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;ClippingRankSum=0.385;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=215.50;MQ0=0;MQRankSum=-4.840e-01;QD=10.62;ReadPosRankSum=1.08;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
-20	10006404	.	A	C	1434.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.09;MQ0=0;QD=31.87;SOR=0.929	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1448,135,0
-20	10006682	.	T	A	1005.03	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=212.18;MQ0=0;QD=33.50;SOR=0.976	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
+20	10004874	.	A	C	1898.06	.	AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.87;MQ0=0;QD=27.51;SOR=0.859	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,50:50:99:1|1:10004874_A_C:1912,150,0
+20	10004887	.	A	G	579.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.140;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=219.74;MQ0=0;MQRankSum=-3.798e+00;QD=12.33;ReadPosRankSum=1.26;SOR=0.813	GT:AD:DP:GQ:PGT:PID:PL	0/1:27,20:47:99:0|1:10004874_A_C:587,0,795
+20	10005010	.	C	T	1376.06	.	AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=223.84;MQ0=0;QD=29.11;SOR=1.236	GT:AD:DP:GQ:PL	1/1:0,39:39:99:1390,117,0
+20	10005427	.	C	T	1839.06	.	AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.25;MQ0=0;QD=34.06;SOR=0.846	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1853,162,0
+20	10005499	.	A	G	1797.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.87;ClippingRankSum=0.832;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.17;MQ0=0;MQRankSum=2.05;QD=32.67;ReadPosRankSum=1.82;SOR=0.730	GT:AD:DP:GQ:PL	1/1:2,53:55:99:1811,116,0
+20	10005587	.	A	G	821.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.474;ClippingRankSum=0.831;DP=53;ExcessHet=3.0103;FS=2.345;MLEAC=1;MLEAF=0.500;MQ=218.96;MQ0=0;MQRankSum=-3.660e-01;QD=15.50;ReadPosRankSum=-1.671e+00;SOR=0.516	GT:AD:DP:GQ:PL	0/1:24,29:53:99:829,0,639
+20	10005723	.	A	G	1461.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.83;MQ0=0;QD=31.09;SOR=1.132	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1475,140,0
+20	10006291	.	G	A	456.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;ClippingRankSum=0.385;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=215.50;MQ0=0;MQRankSum=-4.840e-01;QD=10.62;ReadPosRankSum=1.08;SOR=0.583	GT:AD:DP:GQ:PL	0/1:26,17:43:99:464,0,692
+20	10006404	.	A	C	1434.06	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.09;MQ0=0;QD=31.87;SOR=0.929	GT:AD:DP:GQ:PL	1/1:0,45:45:99:1448,135,0
+20	10006682	.	T	A	1005.06	.	AC=2;AF=1.00;AN=2;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=212.18;MQ0=0;QD=33.50;SOR=0.976	GT:AD:DP:GQ:PL	1/1:0,30:30:90:1019,90,0
 20	10006819	.	AAAAC	A	1509.03	.	AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.67;MQ0=0;QD=28.08;SOR=1.675	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1523,106,0
-20	10007150	.	G	C	527.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.780e-01;ClippingRankSum=0.628;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.879;QD=19.54;ReadPosRankSum=0.377;SOR=2.122	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,17:27:99:0|1:10007150_G_C:535,0,357
-20	10007175	.	C	T	261.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.425;ClippingRankSum=-7.080e-01;DP=25;ExcessHet=3.0103;FS=4.008;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=1.50;QD=10.46;ReadPosRankSum=1.33;SOR=0.525	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,9:25:99:1|0:10007150_G_C:269,0,592
-20	10007352	.	C	T	1475.03	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.78;MQ0=0;QD=34.30;SOR=0.836	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1489,129,0
-20	10007531	.	A	G	1654.03	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=1.051	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
-20	10007980	.	A	C	1658.03	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.22;MQ0=0;QD=33.16;SOR=0.773	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
-20	10008029	.	T	TA	1212.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.92;ClippingRankSum=-6.590e-01;DP=52;ExcessHet=3.0103;FS=2.943;MLEAC=2;MLEAF=1.00;MQ=208.62;MQ0=0;MQRankSum=1.92;QD=25.79;ReadPosRankSum=1.87;SOR=0.184	GT:AD:DP:GQ:PL	1/1:2,45:47:84:1226,84,0
+20	10007150	.	G	C	527.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.780e-01;ClippingRankSum=0.628;DP=28;ExcessHet=3.0103;FS=9.966;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=0.879;QD=19.54;ReadPosRankSum=0.377;SOR=2.122	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,17:27:99:0|1:10007150_G_C:535,0,357
+20	10007175	.	C	T	261.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.425;ClippingRankSum=-7.080e-01;DP=25;ExcessHet=3.0103;FS=4.008;MLEAC=1;MLEAF=0.500;MQ=225.06;MQ0=0;MQRankSum=1.50;QD=10.47;ReadPosRankSum=1.33;SOR=0.525	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,9:25:99:1|0:10007150_G_C:269,0,592
+20	10007352	.	C	T	1475.06	.	AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=219.78;MQ0=0;QD=34.30;SOR=0.836	GT:AD:DP:GQ:PL	1/1:0,43:43:99:1489,129,0
+20	10007531	.	A	G	1654.06	.	AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.14;MQ0=0;QD=33.08;SOR=1.051	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1668,150,0
+20	10007980	.	A	C	1658.06	.	AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.22;MQ0=0;QD=33.16;SOR=0.773	GT:AD:DP:GQ:PL	1/1:0,50:50:99:1672,150,0
+20	10008029	.	T	TA	1212.03	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.92;ClippingRankSum=-6.590e-01;DP=52;ExcessHet=3.0103;FS=2.943;MLEAC=2;MLEAF=1.00;MQ=208.62;MQ0=0;MQRankSum=1.92;QD=25.79;ReadPosRankSum=1.87;SOR=0.184	GT:AD:DP:GQ:PL	1/1:2,45:47:84:1226,84,0
 20	10008146	.	TA	T	1450.03	.	AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=210.35;MQ0=0;QD=30.85;SOR=0.919	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1464,141,0
-20	10008221	.	T	C	1821.03	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.72;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1835,162,0
-20	10008458	.	T	G	1625.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.58;SOR=1.132	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1639,141,0
-20	10008742	.	G	T	218.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=-5.310e-01;DP=23;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=107.46;MQ0=0;MQRankSum=0.694;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
-20	10008758	.	C	CA	372.06	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.96;MQ0=0;QD=24.80;SOR=1.112	GT:AD:DP:GQ:PL	1/1:0,15:15:48:386,48,0
-20	10008921	.	C	CA	260.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.626;ClippingRankSum=1.62;DP=30;ExcessHet=3.0103;FS=1.707;MLEAC=1;MLEAF=0.500;MQ=144.58;MQ0=0;MQRankSum=0.626;QD=11.85;ReadPosRankSum=-7.580e-01;SOR=0.368	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,12:22:99:0|1:10008921_C_CA:268,0,191
+20	10008221	.	T	C	1821.06	.	AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=215.17;MQ0=0;QD=33.72;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,54:54:99:1835,162,0
+20	10008458	.	T	G	1625.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=222.93;MQ0=0;QD=34.58;SOR=1.132	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1639,141,0
+20	10008742	.	G	T	218.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.08;ClippingRankSum=-5.310e-01;DP=23;ExcessHet=3.0103;FS=11.563;MLEAC=1;MLEAF=0.500;MQ=107.46;MQ0=0;MQRankSum=0.694;QD=11.51;ReadPosRankSum=-1.429e+00;SOR=1.155	GT:AD:DP:GQ:PL	0/1:10,9:19:99:226,0,251
+20	10008758	.	C	CA	372.03	.	AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=91.96;MQ0=0;QD=24.80;SOR=1.112	GT:AD:DP:GQ:PL	1/1:0,15:15:48:386,48,0
+20	10008921	.	C	CA	260.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.626;ClippingRankSum=1.62;DP=30;ExcessHet=3.0103;FS=1.707;MLEAC=1;MLEAF=0.500;MQ=144.58;MQ0=0;MQRankSum=0.626;QD=11.85;ReadPosRankSum=-7.580e-01;SOR=0.368	GT:AD:DP:GQ:PGT:PID:PL	0/1:10,12:22:99:0|1:10008921_C_CA:268,0,191
 20	10008948	.	TA	T	1030.03	.	AC=2;AF=1.00;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=167.56;MQ0=0;QD=23.23;SOR=2.215	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,25:25:75:1|1:10008921_C_CA:1044,75,0
-20	10008952	.	CACACACACACA	C,CCACACACACA	964.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=167.56;MQ0=0;QD=29.03;SOR=3.056	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:981,348,341,516,0,477
-20	10009227	.	A	G	875.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-3.800e-01;DP=62;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.96;MQ0=0;MQRankSum=-1.290e+00;QD=14.59;ReadPosRankSum=1.63;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
-20	10009246	.	A	G	2042.03	.	AC=2;AF=1.00;AN=2;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.08;MQ0=0;QD=33.48;SOR=1.107	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2056,183,0
-20	10009400	.	T	A	1618.03	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.43;SOR=0.735	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1632,141,0
-20	10009512	.	C	G	1516.03	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
-20	10009719	.	A	G	1091.03	.	AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.74;MQ0=0;QD=31.17;SOR=0.869	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
-20	10009795	.	A	G	1171.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=30.67;SOR=0.880	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
-20	10009842	.	G	GAA	501.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.72;ClippingRankSum=-1.506e+00;DP=36;ExcessHet=3.0103;FS=5.649;MLEAC=1;MLEAF=0.500;MQ=186.87;MQ0=0;MQRankSum=-1.549e+00;QD=17.30;ReadPosRankSum=0.065;SOR=1.184	GT:AD:DP:GQ:PL	0/1:15,14:29:99:509,0,580
-20	10009844	.	G	A	572.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.640e+00;ClippingRankSum=0.196;DP=36;ExcessHet=3.0103;FS=5.649;MLEAC=1;MLEAF=0.500;MQ=186.87;MQ0=0;MQRankSum=1.51;QD=19.74;ReadPosRankSum=0.327;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,15:29:99:0|1:10009844_G_A:580,0,533
-20	10009871	.	A	G	566.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364e+00;ClippingRankSum=0.336;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=18.28;ReadPosRankSum=1.44;SOR=0.829	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,15:31:99:0|1:10009844_G_A:574,0,602
+20	10008952	.	CACACACACACA	C,CCACACACACA	964.02	.	AC=1,1;AF=0.500,0.500;AN=2;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=167.56;MQ0=0;QD=29.03;SOR=3.056	GT:AD:DP:GQ:PL	1/2:0,12,9:21:99:981,348,341,516,0,477
+20	10009227	.	A	G	875.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.320e+00;ClippingRankSum=-3.800e-01;DP=62;ExcessHet=3.0103;FS=3.616;MLEAC=1;MLEAF=0.500;MQ=223.96;MQ0=0;MQRankSum=-1.290e+00;QD=14.59;ReadPosRankSum=1.63;SOR=1.244	GT:AD:DP:GQ:PL	0/1:26,34:60:99:883,0,770
+20	10009246	.	A	G	2042.06	.	AC=2;AF=1.00;AN=2;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=224.08;MQ0=0;QD=33.48;SOR=1.107	GT:AD:DP:GQ:PL	1/1:0,61:61:99:2056,183,0
+20	10009400	.	T	A	1618.06	.	AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=218.72;MQ0=0;QD=34.43;SOR=0.735	GT:AD:DP:GQ:PL	1/1:0,47:47:99:1632,141,0
+20	10009512	.	C	G	1516.06	.	AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=221.12;MQ0=0;QD=32.96;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,46:46:99:1530,138,0
+20	10009719	.	A	G	1091.06	.	AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=211.74;MQ0=0;QD=31.17;SOR=0.869	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1105,105,0
+20	10009795	.	A	G	1171.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=192.53;MQ0=0;QD=30.67;SOR=0.880	GT:AD:DP:GQ:PL	1/1:0,33:33:99:1185,99,0
+20	10009842	.	G	GAA	501.60	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.72;ClippingRankSum=-1.506e+00;DP=36;ExcessHet=3.0103;FS=5.649;MLEAC=1;MLEAF=0.500;MQ=186.87;MQ0=0;MQRankSum=-1.549e+00;QD=17.30;ReadPosRankSum=0.065;SOR=1.184	GT:AD:DP:GQ:PL	0/1:15,14:29:99:509,0,580
+20	10009844	.	G	A	572.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.640e+00;ClippingRankSum=0.196;DP=36;ExcessHet=3.0103;FS=5.649;MLEAC=1;MLEAF=0.500;MQ=186.87;MQ0=0;MQRankSum=1.51;QD=19.75;ReadPosRankSum=0.327;SOR=0.876	GT:AD:DP:GQ:PGT:PID:PL	0/1:14,15:29:99:0|1:10009844_G_A:580,0,533
+20	10009871	.	A	G	566.64	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364e+00;ClippingRankSum=0.336;DP=38;ExcessHet=3.0103;FS=8.080;MLEAC=1;MLEAF=0.500;MQ=190.43;MQ0=0;MQRankSum=1.05;QD=18.28;ReadPosRankSum=1.44;SOR=0.829	GT:AD:DP:GQ:PGT:PID:PL	0/1:16,15:31:99:0|1:10009844_G_A:574,0,602
 20	10009875	.	A	G,AGGGAGG	1537.06	.	AC=1,1;AF=0.500,0.500;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=192.56;MQ0=0;QD=26.61;SOR=1.329	GT:AD:DP:GQ:PL	1/2:0,14,14:28:99:1554,625,572,612,0,543
-20	10009879	.	A	G	1471.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.10;MQ0=0;QD=29.20;SOR=0.880	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,33:33:99:1|1:10009879_A_G:1485,99,0
-20	10009883	.	A	G	1471.03	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.10;MQ0=0;QD=28.55;SOR=0.880	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,33:33:99:1|1:10009879_A_G:1485,99,0
+20	10009879	.	A	G	1471.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.10;MQ0=0;QD=29.20;SOR=0.880	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,33:33:99:1|1:10009879_A_G:1485,99,0
+20	10009883	.	A	G	1471.06	.	AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=193.10;MQ0=0;QD=28.55;SOR=0.880	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,33:33:99:1|1:10009879_A_G:1485,99,0