diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort.java
index 821ebffb587..75105026a09 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort.java
@@ -1,9 +1,7 @@
 package org.broadinstitute.hellbender.tools.variantdb.nextgen;
 
-import htsjdk.variant.vcf.VCFFilterHeaderLine;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.apache.avro.generic.GenericRecord;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.barclay.argparser.Advanced;
@@ -13,12 +11,9 @@
 import org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.tools.variantdb.CommonCode;
-import org.broadinstitute.hellbender.tools.variantdb.nextgen.FilterSensitivityTools;
 import org.broadinstitute.hellbender.tools.variantdb.SampleList;
 import org.broadinstitute.hellbender.tools.variantdb.SchemaUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
-import org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader;
-import org.broadinstitute.hellbender.utils.bigquery.TableReference;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 
 import java.util.*;
@@ -52,13 +47,15 @@ public class ExtractCohort extends ExtractTool {
     @Argument(
             fullName = "cohort-extract-table",
             doc = "Fully qualified name of the table where the cohort data exists (already subsetted)",
-            optional = false
+            mutex = {"cohort-avro-file-name"},
+            optional = true
     )
     private String cohortTable = null;
 
     @Argument(
             fullName = "cohort-avro-file-name",
             doc = "Path of the cohort avro file",
+            mutex = {"cohort-extract-table"},
             optional = true
     )
     private String cohortAvroFileName = null;
@@ -79,31 +76,31 @@ public class ExtractCohort extends ExtractTool {
 
 
     @Argument(
-            fullName="snps-truth-sensitivity-filter-level",
-            doc="The truth sensitivity level at which to start filtering SNPs",
-            optional=true
+            fullName ="snps-truth-sensitivity-filter-level",
+            doc = "The truth sensitivity level at which to start filtering SNPs",
+            optional = true
     )
     private Double truthSensitivitySNPThreshold = null;
 
     @Argument(
-            fullName="indels-truth-sensitivity-filter-level",
-            doc="The truth sensitivity level at which to start filtering INDELs",
-            optional=true
+            fullName = "indels-truth-sensitivity-filter-level",
+            doc = "The truth sensitivity level at which to start filtering INDELs",
+            optional = true
     )
     private Double truthSensitivityINDELThreshold = null;
 
     @Advanced
     @Argument(
-            fullName="snps-lod-score-cutoff",
-            doc="The VQSLOD score below which to start filtering SNPs",
-            optional=true)
+            fullName = "snps-lod-score-cutoff",
+            doc = "The VQSLOD score below which to start filtering SNPs",
+            optional = true)
     private Double vqsLodSNPThreshold = null;
 
     @Advanced
     @Argument(
-            fullName="indels-lod-score-cutoff",
-            doc="The VQSLOD score below which to start filtering INDELs",
-            optional=true)
+            fullName = "indels-lod-score-cutoff",
+            doc = "The VQSLOD score below which to start filtering INDELs",
+            optional = true)
     private Double vqsLodINDELThreshold = null;
 
 
@@ -145,6 +142,20 @@ protected void onStartup() {
             throw new UserException("min-location and max-location should not be used together with intervals (-L).");
         }
 
+        // if there is a avro file, the BQ specific parameters are unnecessary,
+        // but they all are required if there is no avro file
+        if (cohortAvroFileName == null && (projectID == null || cohortTable == null)) {
+            throw new UserException("Project id (--project-id) and cohort table (--cohort-extract-table) are required " +
+                "if no avro file (--cohort-avro-file-name) is provided.");
+        }
+
+        // if there is a sample file, the BQ specific parameters are unnecessary,
+        // but without a sample file, both a sample-table and a project-id are needed
+        if (sampleFileName == null && (projectID == null || sampleTableName == null)) {
+            throw new UserException("Project id (--project-id) and sample table (--sample-table) are required " +
+                "if no sample file (--sample-file) is provided.");
+        }
+
         engine = new ExtractCohortEngine(
                 projectID,
                 vcfWriter,
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java
index 61e99b612c8..6f46b00fe26 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java
@@ -103,7 +103,7 @@ public ExtractCohortEngine(final String projectID,
         this.sampleNames = sampleNames;
         this.mode = mode;
 
-        this.cohortTableRef = new TableReference(cohortTableName, SchemaUtils.COHORT_FIELDS);
+        this.cohortTableRef = cohortTableName == null || "".equals(cohortTableName) ? null : new TableReference(cohortTableName, SchemaUtils.COHORT_FIELDS);
         this.cohortAvroFileName = cohortAvroFileName;
         this.traversalIntervals = traversalIntervals;
         this.minLocation = minLocation;
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractTool.java b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractTool.java
index 6e9fe318996..1f6c9fa0266 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractTool.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractTool.java
@@ -46,21 +46,24 @@ public enum QueryMode {
     @Argument(
             fullName = "project-id",
             doc = "ID of the Google Cloud project to use when executing queries",
-            optional = false
+            optional = true
     )
     protected String projectID = null;
 
     @Argument(
             fullName = "sample-table",
             doc = "Fully qualified name of a bigquery table containing a single column `sample` that describes the full list of samples to extract",
-            optional = true
+            optional = true,
+            mutex={"sample-file"}
     )
     protected String sampleTableName = null;
 
     @Argument(
             fullName = "sample-file",
             doc = "Alternative to `sample-table`. Pass in a (sample_id,sample_name) CSV that describes the full list of samples to extract. No header",
-            optional = true
+            optional = true,
+            mutex={"sample-table"}
+
     )
     protected File sampleFileName = null;
 
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortTest.java b/src/test/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortTest.java
new file mode 100644
index 00000000000..85f51cd964c
--- /dev/null
+++ b/src/test/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortTest.java
@@ -0,0 +1,42 @@
+package org.broadinstitute.hellbender.tools.variantdb.nextgen;
+
+import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
+import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+
+class ExtractCohortTest extends CommandLineProgramTest {
+  private final String prefix = getToolTestDataDir();
+  private final String cohortAvroFileName = prefix +"chr20_subset_3_samples.avro";
+  private final String sampleFile = prefix +"sample_list";
+
+  @Test
+  public void testFinalVCFfromAvro() throws Exception {
+    // To create the expectedVCF file (of expected output) --create a temp table in BQ with the following query
+    // and then export it through the BQ GUI as an avro file into GCS.
+    // SELECT * FROM `spec-ops-aou.anvil_100_for_testing.exported_cohort_all_samples`
+    // where location < 20000000200000 and location >= 20000000100000
+    // and (sample_name="HG00405" or sample_name="HG00418" or sample_name="HG00408")
+    final File expectedVCF = getTestFile("expected.vcf");
+
+    // create a temporary file (that will get cleaned up after the test has run) to hold the output data in
+    final File outputVCF = createTempFile("output", "vcf");
+
+    final ArgumentsBuilder args = new ArgumentsBuilder();
+    args
+        .add("mode", "GENOMES")
+        .add("ref-version", 38)
+        .add("query-mode", "LOCAL_SORT")
+        .add("R", hg38Reference)
+        .add("O", outputVCF.getAbsolutePath())
+        .add("local-sort-max-records-in-ram", 10000000)
+        .add("cohort-avro-file-name", cohortAvroFileName)
+        .add("sample-file", sampleFile);
+
+    runCommandLine(args);
+    IntegrationTestSpec.assertEqualTextFiles(outputVCF, expectedVCF);
+  }
+}
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/chr20_subset_3_samples.avro b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/chr20_subset_3_samples.avro
new file mode 100644
index 00000000000..ae9338fdb51
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/chr20_subset_3_samples.avro differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/expected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/expected.vcf
new file mode 100644
index 00000000000..65df09ddc99
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/expected.vcf
@@ -0,0 +1,3699 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=EXCESS_ALLELES,Description="Site has an excess (>6) of alternate alleles">
+##FILTER=<ID=ExcessHet,Description="Site has excess het value larger than the threshold">
+##FILTER=<ID=NAY,Description="Considered a NAY in the Yay, Nay, Grey table">
+##FILTER=<ID=NO_HQ_GENOTYPES,Description="Site has no high quality variant genotypes">
+##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">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##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)">
+##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_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_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">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
+##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic raw data for Mapping Quality Rank Sum">
+##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. 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=AS_VQSLOD,Number=A,Type=String,Description="For each alt allele, the log odds of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format">
+##INFO=<ID=AS_YNG,Number=A,Type=String,Description="For each alt allele, the yay/nay/grey status (yay are known good alleles, nay are known false positives, grey are unknown)">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=SB_TABLE,Number=4,Type=Integer,Description="Forward/reverse read counts for strand bias tests">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##contig=<ID=chr1,length=248956422,assembly=38>
+##contig=<ID=chr2,length=242193529,assembly=38>
+##contig=<ID=chr3,length=198295559,assembly=38>
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+##contig=<ID=HLA-DRB1*08:03:02,length=13562,assembly=38>
+##contig=<ID=HLA-DRB1*09:21,length=16039,assembly=38>
+##contig=<ID=HLA-DRB1*10:01:01,length=13501,assembly=38>
+##contig=<ID=HLA-DRB1*11:01:01,length=13921,assembly=38>
+##contig=<ID=HLA-DRB1*11:01:02,length=13931,assembly=38>
+##contig=<ID=HLA-DRB1*11:04:01,length=13919,assembly=38>
+##contig=<ID=HLA-DRB1*12:01:01,length=13404,assembly=38>
+##contig=<ID=HLA-DRB1*12:17,length=11260,assembly=38>
+##contig=<ID=HLA-DRB1*13:01:01,length=13935,assembly=38>
+##contig=<ID=HLA-DRB1*13:02:01,length=13941,assembly=38>
+##contig=<ID=HLA-DRB1*14:05:01,length=13933,assembly=38>
+##contig=<ID=HLA-DRB1*14:54:01,length=13936,assembly=38>
+##contig=<ID=HLA-DRB1*15:01:01:01,length=11080,assembly=38>
+##contig=<ID=HLA-DRB1*15:01:01:02,length=11571,assembly=38>
+##contig=<ID=HLA-DRB1*15:01:01:03,length=11056,assembly=38>
+##contig=<ID=HLA-DRB1*15:01:01:04,length=11056,assembly=38>
+##contig=<ID=HLA-DRB1*15:02:01,length=10313,assembly=38>
+##contig=<ID=HLA-DRB1*15:03:01:01,length=11567,assembly=38>
+##contig=<ID=HLA-DRB1*15:03:01:02,length=11569,assembly=38>
+##contig=<ID=HLA-DRB1*16:02:01,length=11005,assembly=38>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00405	HG00408	HG00418
+chr20	100014	.	A	G	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:87:983	1/1:96:1112	1/1:99:1127
+chr20	101341	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1240	0/0:60	0/0:60
+chr20	101371	.	T	C	.	.	AC=5;AF=0.833;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1137	1/1:99:1288	0/1:99:541
+chr20	101433	.	A	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:90:1319	0/1:99:982
+chr20	101438	.	G	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:90:1319	0/1:99:1011
+chr20	101505	.	A	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:486
+chr20	101563	.	T	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:702
+chr20	101576	.	G	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1216	0/1:99:551
+chr20	102609	.	CTGTGTGTGTG	CTCTGTGTGTGTGTG,C,CTG	.	.	AC=2,1,3;AF=0.333,0.167,0.500;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:18:327	2/3:99:1333	3/3:94:1382
+chr20	102619	.	G	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:50	0/1:99:775	1/1:93:1382
+chr20	102621	.	G	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:50	0/1:99:236	0/0:60
+chr20	102623	.	G	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:50	0/1:99:475	0/0:60
+chr20	102634	.	T	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	0/1:99:743	1/1:96:1409
+chr20	104475	.	C	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:617	0/0:60
+chr20	105364	.	CA	C	.	.	AC=1;AF=0.250;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	0/0:20	0/1:99:312	./.
+chr20	106471	.	G	A	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:555	0/0:60
+chr20	106775	.	A	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:709	0/0:60
+chr20	109367	.	C	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	0/1:99:292	1/1:90:998
+chr20	110447	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1334	1/1:96:1112
+chr20	110867	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1504	1/1:99:1887
+chr20	111066	.	C	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:647
+chr20	111725	.	A	G	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:694
+chr20	111886	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:50	1/1:93:1078	1/1:99:1479
+chr20	113005	.	CT	CTTTTTT,C	.	.	AC=1,1;AF=0.167,0.167;AN=6;ExcessHet=3.9794	GT:GQ:RGQ	0/1:21:21	0/0:30	0/2:66:86
+chr20	113297	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1147	0/0:60	0/0:60
+chr20	114540	.	CT	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/1:99:309	0/0:60	0/0:60
+chr20	115682	.	A	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:374	0/0:60
+chr20	115683	.	A	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:374	0/0:60
+chr20	120721	.	G	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1136	0/1:99:790
+chr20	121439	.	TATTCTTCAGCTGTCAAA	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:732
+chr20	121787	.	C	A	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/1:99:480	0/0:60	0/0:60
+chr20	124383	.	AT	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:63:543	0/1:99:295
+chr20	125389	.	CAGAGT	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:605
+chr20	126062	.	C	CT	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:39:319	1/1:72:587	1/1:93:776
+chr20	127687	.	A	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:81:928	1/1:99:1504
+chr20	128317	.	A	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:652
+chr20	128517	.	C	CA,CAAA	.	.	AC=3,1;AF=0.750,0.250;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	./.	1/1:17:100	1/2:83:274
+chr20	130329	.	G	A	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:534
+chr20	130338	.	A	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1935	1/1:99:1759
+chr20	130339	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1935	1/1:99:1759
+chr20	131163	.	G	A	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:50	0/0:50	0/1:99:233
+chr20	132236	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1470	0/1:99:415
+chr20	135387	.	G	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:40	1/1:36:406	0/1:99:166
+chr20	139481	.	A	AAG	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1485	1/1:99:1450
+chr20	140109	.	C	CAATT	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1584	1/1:99:1518
+chr20	143010	.	G	GT	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:962	0/1:99:277
+chr20	144480	.	C	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:383
+chr20	145669	.	ACC	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=3.9794	GT:GQ:RGQ	0/1:99:514	0/0:60	0/1:99:550
+chr20	145888	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=3.9794	GT:GQ:RGQ	0/0:60	0/1:99:486	0/1:99:667
+chr20	145959	.	C	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1915	0/1:99:552
+chr20	145973	.	T	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1949	0/1:99:590
+chr20	146089	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:84:928	0/1:99:379
+chr20	146119	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:72:808	0/1:99:361
+chr20	146282	.	C	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1560	0/1:99:751
+chr20	146289	.	A	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1525	0/1:99:775
+chr20	147079	.	A	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1286	0/1:99:641
+chr20	147311	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:96:1077	0/0:60	0/0:60
+chr20	148072	.	C	G	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1172	0/1:99:501
+chr20	148222	.	G	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1217	0/0:60	0/0:60
+chr20	148422	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:96:1102	0/0:60	0/0:60
+chr20	148972	.	G	A	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1331	1/1:99:1413	1/1:99:1603
+chr20	148994	.	A	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:626
+chr20	149095	.	G	GGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGACCCATATTTGGGAA	.	.	AC=2;AF=0.500;AN=4;ExcessHet=0.7918	GT:GQ:RGQ	0/0:60	1/1:93:975	./.
+chr20	149223	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1256	0/1:99:537
+chr20	149492	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=3.9794	GT:GQ:RGQ	0/0:60	0/1:99:562	0/1:99:387
+chr20	150721	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:96:1113	0/1:99:495
+chr20	150854	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:78:894	1/1:78:904	1/1:81:939
+chr20	150864	.	CTCT	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:78:1137	0/1:99:558
+chr20	151016	.	A	G	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:96:1067	1/1:95:1036	1/1:99:1271
+chr20	151307	.	C	CCA	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:67:1179	0/1:99:335
+chr20	151663	.	TA	T	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:72:677	1/1:63:591	1/1:84:770
+chr20	152134	.	T	C	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/0:60	0/1:99:523
+chr20	152450	.	CAAA	C,CAAAA,AAAA	.	.	AC=3,2,1;AF=0.500,0.333,0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:66:970	2/3:20:351	1/2:99:755
+chr20	152517	.	T	A	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1195	1/1:69:800	1/1:96:1092
+chr20	152792	.	A	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	1/1:99:1361	0/0:60	0/1:99:544
+chr20	152876	.	GT	G	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:321	0/0:60
+chr20	153098	.	G	GT	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	1/1:99:1182	0/0:60	0/1:99:614
+chr20	153259	.	C	G	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	1/1:84:963	0/0:60	0/1:99:555
+chr20	153376	.	A	G	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/0:60	1/1:99:1215	0/1:99:655
+chr20	153555	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	1/1:75:869	0/0:60	0/1:99:474
+chr20	153640	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:1170	0/0:60	0/0:60
+chr20	153643	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:78:1170	1/1:99:1211	1/1:96:1112
+chr20	153686	.	C	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/1:99:377	0/0:60	0/0:60
+chr20	153725	.	A	G	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:81:929	1/1:93:1038	1/1:93:1017
+chr20	153759	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1469	0/0:60	1/1:93:1363
+chr20	153780	.	C	T	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1565	1/1:99:1547	1/1:99:1620
+chr20	153787	.	CAAAAAAAAA	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1575	1/1:99:1490	1/1:99:1755
+chr20	153835	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:93:1057	1/1:96:1102	1/1:99:1634
+chr20	153898	.	A	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:894	0/0:60	1/1:99:1520
+chr20	154002	.	C	T	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:78:883	1/1:99:1249	1/1:99:1160
+chr20	154128	.	T	TA	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:25:308	0/0:60	1/1:99:844
+chr20	154203	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:72:804	1/1:84:933	1/1:99:1270
+chr20	154290	.	T	G	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1219	1/1:93:1053	1/1:99:1538
+chr20	154474	.	G	GTT	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:98:1483	1/1:99:1754	1/1:99:1845
+chr20	154477	.	C	CAT	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1485	1/1:99:1800	1/1:99:1890
+chr20	154479	.	C	CACAGGAAGACTATAAATAACT	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1942	1/1:99:1934	1/1:99:2115
+chr20	154847	.	C	T	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1460	1/1:99:1425	1/1:99:1252
+chr20	155384	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1231	0/0:60	1/1:99:1157
+chr20	155733	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1529	0/0:60	1/1:99:1251
+chr20	155813	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1207	0/0:60	1/1:93:1078
+chr20	156080	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1276	0/0:60	1/1:87:982
+chr20	156287	.	G	GA	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:90:871	0/0:60	1/1:99:1305
+chr20	156473	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:75:869	0/0:60	1/1:93:1068
+chr20	156486	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1773	0/0:60
+chr20	156669	.	C	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:60:685	0/0:60	1/1:99:1331
+chr20	156813	.	T	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1157	0/0:60	1/1:99:1356
+chr20	156877	.	GTA	G	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:78:1150	1/1:99:1321	1/1:99:1530
+chr20	156881	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:63:787	0/0:60	1/1:93:1160
+chr20	157033	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:93:1096	0/0:60
+chr20	157259	.	T	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1231	0/0:60	1/1:99:1599
+chr20	157292	.	C	G	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1162	1/1:87:1008	1/1:99:1469
+chr20	157363	.	G	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:93:1078	1/1:99:1405	1/1:99:1439
+chr20	157484	.	G	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:93:1078	0/0:60	1/1:99:1479
+chr20	157507	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1182	0/0:20	1/1:99:1633
+chr20	157537	.	GC	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1424	0/0:60
+chr20	157819	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:904	0/0:60	1/1:99:1190
+chr20	157914	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:84:1216	0/0:30	1/1:99:1625
+chr20	157927	.	ATATATGTG	A	.	.	AC=4;AF=1.00;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	1/1:75:1125	./.	1/1:99:1735
+chr20	157929	.	ATATGTGTG	A	.	.	AC=2;AF=1.00;AN=2;ExcessHet=3.0103	GT:GQ:RGQ	./.	1/1:99:1440	./.
+chr20	157960	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:20	1/1:99:1609	0/0:40
+chr20	157962	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1575	0/0:60
+chr20	157965	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:1170	0/0:60	1/1:93:1395
+chr20	157974	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:1160	0/0:60	1/1:96:1440
+chr20	157979	.	A	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:1160	0/0:60	1/1:90:1350
+chr20	158513	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1222	0/0:60	1/1:99:1107
+chr20	158532	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:96:1087	0/0:60	1/1:87:968
+chr20	158721	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1166	0/0:60
+chr20	158768	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1286	0/0:60	1/1:99:1424
+chr20	158815	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:93:1078	0/0:60	1/1:99:1356
+chr20	158935	.	C	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1391	0/0:60	1/1:78:893
+chr20	159104	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1239	1/1:99:1564	1/1:90:1043
+chr20	159200	.	A	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1717	0/0:60
+chr20	159274	.	T	TAAAAAA,TAA	.	.	AC=4,2;AF=0.667,0.333;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:78:1148	2/2:87:1044	1/1:87:1273
+chr20	159286	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:84:1216	0/0:60	1/1:99:1508
+chr20	159445	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1220	0/0:60
+chr20	159495	.	G	GAATGGCATAAACT	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1800	0/0:60	1/1:99:1530
+chr20	159530	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:84:993	0/0:60	1/1:99:1321
+chr20	159639	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:93:1042	0/0:60
+chr20	159755	.	TTTG	T	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:52:752	1/1:99:1654	1/1:99:1565
+chr20	159864	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1529	0/0:60	1/1:99:1709
+chr20	159865	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1529	0/0:60	1/1:99:1709
+chr20	159952	.	AG	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:96:1288	0/0:60	1/1:99:1935
+chr20	160054	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:84:973	0/0:60	1/1:99:1146
+chr20	160212	.	C	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:93:1043	0/0:60	1/1:69:787
+chr20	160282	.	G	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:51:566	0/0:60	1/1:63:711
+chr20	160312	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:21:243	0/0:60	1/1:51:496
+chr20	160384	.	G	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:18:260	0/0:60	1/1:27:394
+chr20	160388	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:18:260	0/0:60	1/1:24:360
+chr20	160408	.	G	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/1:27:197	0/0:60	1/1:24:360
+chr20	160413	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/1:27:197	0/0:60	1/1:24:360
+chr20	160433	.	G	A	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/1:10:204	0/0:60	1/1:30:318
+chr20	160558	.	C	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:27:290	0/0:60	1/1:24:238
+chr20	160625	.	T	C	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/1:12:94	0/0:60	1/1:24:233
+chr20	160727	.	T	G	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/1:38:165	0/0:60	1/1:15:225
+chr20	160731	.	C	T	.	.	AC=3;AF=0.500;AN=6;ExcessHet=1.5490	GT:GQ:RGQ	0/1:38:165	0/0:60	1/1:18:259
+chr20	160873	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:21:238	0/0:60	1/1:15:174
+chr20	160889	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:27:308	0/0:60	1/1:21:242
+chr20	160956	.	T	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:30:342	0/0:60	1/1:45:511
+chr20	160967	.	G	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:36:411	0/0:60	1/1:45:522
+chr20	161128	.	G	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:66:753	0/0:60	1/1:78:877
+chr20	161181	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:63:723	0/0:60	1/1:51:591
+chr20	161221	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:51:565	0/0:60	1/1:60:692
+chr20	161380	.	G	A	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:27:313	1/1:75:854	1/1:45:516
+chr20	161451	.	C	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:33:381	0/0:60	1/1:30:338
+chr20	161571	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:15:194	0/0:20	1/1:18:250
+chr20	161588	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:9:125	1/1:24:257	1/1:12:180
+chr20	161621	.	C	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:9:125	0/0:30	1/1:9:125
+chr20	161638	.	C	A	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:6:90	1/1:39:399	1/1:9:125
+chr20	161698	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:15:156	0/0:50	1/1:6:62
+chr20	161730	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:9:135	0/0:50	1/1:6:90
+chr20	161734	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:9:135	0/0:50	1/1:6:90
+chr20	161770	.	G	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:15:152	0/0:50	1/1:18:184
+chr20	161914	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:21:241	0/0:10	1/1:27:302
+chr20	161918	.	C	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:10	1/1:48:476	0/0:20
+chr20	161991	.	G	C	.	.	AC=1;AF=0.250;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	./.	0/0:60	0/1:32:112
+chr20	162023	.	A	C	.	.	AC=1;AF=0.250;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	0/1:54:72	0/0:20	./.
+chr20	162035	.	A	G	.	.	AC=1;AF=0.250;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	0/1:54:72	0/0:20	./.
+chr20	162151	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:9:104	1/1:36:326	1/1:18:202
+chr20	162268	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=3.9794	GT:GQ:RGQ	0/1:47:47	0/0:60	0/1:35:80
+chr20	162455	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:24:247	0/0:30	1/1:36:414
+chr20	162806	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:40	1/1:63:719	0/0:50
+chr20	162854	.	G	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:30:348	0/0:30	1/1:39:452
+chr20	162932	.	G	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:39:452	0/0:60	1/1:33:362
+chr20	163082	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:57:615	0/0:60	1/1:99:1399
+chr20	163113	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:78:884	0/0:60	1/1:99:1245
+chr20	163277	.	C	T	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:83:921	1/1:83:878	1/1:99:1273
+chr20	163741	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1206	0/0:60
+chr20	163894	.	A	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1627	0/0:60
+chr20	163919	.	T	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1520	0/0:60
+chr20	163929	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1543	0/0:60
+chr20	164191	.	C	CT	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1390	0/0:60
+chr20	164243	.	CCTT	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1562	0/0:60
+chr20	164258	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1180	0/0:60
+chr20	164569	.	G	A	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:81:919	1/1:84:971	1/1:72:834
+chr20	164616	.	G	GC	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1414	0/0:60
+chr20	164772	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:78:856	0/0:60
+chr20	165108	.	C	CAT,T	.	.	AC=4,2;AF=0.667,0.333;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:64:1101	2/2:66:874	1/1:79:1371
+chr20	165212	.	C	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:81:913	0/0:60	1/1:99:1265
+chr20	166310	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:90:1018	0/0:60	1/1:99:1127
+chr20	166354	.	A	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1355	0/0:60
+chr20	166554	.	G	A	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:699	0/0:60
+chr20	166856	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:96:1113	0/0:60	1/1:99:1448
+chr20	166960	.	CA	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:991	0/0:60	1/1:99:1351
+chr20	167044	.	A	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1246	0/0:60	1/1:99:1489
+chr20	167274	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:87:1305	0/0:60	1/1:99:1654
+chr20	167276	.	A	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:87:1305	0/0:60	1/1:99:1654
+chr20	167443	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:95:1062	1/1:96:1077	1/1:99:1348
+chr20	167839	.	T	C	.	.	AC=6;AF=1.00;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	1/1:99:1147	1/1:99:1280	1/1:99:1238
+chr20	168062	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:93:1078	0/0:60	1/1:75:869
+chr20	168478	.	CT	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:87:1121	0/0:60	1/1:99:1718
+chr20	168766	.	C	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1599	0/0:60
+chr20	169334	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1499	0/0:60
+chr20	170689	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1286	0/0:60
+chr20	171892	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:96:1087	0/0:60
+chr20	171929	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:81:938	0/0:60
+chr20	172331	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:84:1199	0/0:60
+chr20	172351	.	C	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:81:1154	0/0:60
+chr20	172626	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1574	0/0:60
+chr20	172657	.	T	TTC	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1923	0/0:60
+chr20	172752	.	C	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1216	0/0:60
+chr20	173050	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:96:1131	0/0:60
+chr20	173215	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	0/0:60	1/1:99:1252
+chr20	173973	.	T	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1470	0/0:60
+chr20	175269	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1207	0/0:60
+chr20	175314	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:78:904	0/0:60
+chr20	175524	.	C	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:96:1419	0/0:60
+chr20	175532	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:96:1419	0/0:60
+chr20	175688	.	G	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:93:1394	0/0:60
+chr20	175689	.	G	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:93:1394	0/0:60
+chr20	175893	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:2181	0/0:60
+chr20	175897	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:2181	0/0:60
+chr20	176011	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1473	0/0:60
+chr20	176015	.	A	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1473	0/0:60
+chr20	176516	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:60:693	0/0:60
+chr20	176631	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:87:983	0/0:60
+chr20	177105	.	A	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:87:1008	0/0:60
+chr20	177335	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:75:869	0/0:60
+chr20	177473	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:90:1033	0/0:60
+chr20	177674	.	G	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1231	0/0:60
+chr20	177793	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1122	0/0:60
+chr20	177854	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1216	0/0:60
+chr20	178258	.	C	A	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:311	0/0:60
+chr20	178648	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:81:938	0/0:60
+chr20	179470	.	A	AT	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1130	0/0:60
+chr20	179567	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1177	0/0:60
+chr20	179892	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:90:1043	0/0:60
+chr20	179910	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1146	0/0:60
+chr20	180809	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1355	0/0:60
+chr20	182042	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1122	0/0:60
+chr20	182966	.	A	AAT	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:93:1395	0/0:60
+chr20	183100	.	T	TACACAC	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:75:1125	0/0:60
+chr20	183638	.	G	GAAAAC	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:96:1430	0/0:60
+chr20	183643	.	G	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:96:1430	0/0:60
+chr20	183699	.	A	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1109	0/0:60
+chr20	185267	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1459	0/0:60
+chr20	186086	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:89:992	0/0:60
+chr20	186183	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1316	0/0:60
+chr20	186319	.	C	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:609	0/0:60
+chr20	186669	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1206	0/0:60
+chr20	186790	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:80:878	0/0:60
+chr20	186841	.	A	G	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:249	0/0:60
+chr20	187439	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:87:1008	0/0:60
+chr20	187825	.	T	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1121	0/0:60
+chr20	188087	.	T	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1286	0/0:60
+chr20	189060	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:93:1078	0/0:60
+chr20	189354	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:84:973	0/0:60
+chr20	189557	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1147	0/0:60	0/0:60
+chr20	189948	.	T	C	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1145	0/0:60
+chr20	190001	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1182	0/0:60
+chr20	190548	.	C	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1520	0/0:60
+chr20	190675	.	C	CTT	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:48:471	0/0:10
+chr20	190950	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1197	0/0:60
+chr20	190986	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:99:1147	0/0:60
+chr20	191726	.	CT	CTT,C	.	.	AC=2,2;AF=0.333,0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:55:475	2/2:57:441	0/0:60
+chr20	191877	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:87:988	0/0:60
+chr20	192100	.	G	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:84:972	0/0:60
+chr20	193110	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:78:857	0/0:60
+chr20	193428	.	A	G	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:69:799	0/0:60
+chr20	194746	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	0/0:60	1/1:87:988	0/0:60
+chr20	195745	.	CGTGTGT	CGT,C,CGTGT	.	.	AC=2,1,1;AF=0.333,0.167,0.167;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:57:855	2/3:99:769	0/0:60
+chr20	196106	.	A	T	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:60:695	0/0:60	0/0:60
+chr20	196584	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1122	0/0:60	1/1:87:1008
+chr20	196609	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:96:1077	0/0:60	1/1:81:939
+chr20	197642	.	G	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:514	0/0:60
+chr20	198088	.	G	A	.	.	AC=2;AF=0.333;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1311	0/0:60	0/0:60
+chr20	198171	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1509	0/0:60	1/1:99:1565
+chr20	198174	.	G	A	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1544	0/0:60	1/1:99:1599
+chr20	198215	.	C	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:99:1207	0/0:60	1/1:99:1375
+chr20	198814	.	A	T	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:75:844	0/0:60	1/1:93:1075
+chr20	198921	.	A	G	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:87:998	0/0:60	1/1:99:1246
+chr20	199094	.	TTAAAA	T	.	.	AC=1;AF=0.167;AN=6;ExcessHet=3.0103	GT:GQ:RGQ	0/0:60	0/1:99:351	0/0:60
+chr20	199123	.	T	C	.	.	AC=4;AF=0.667;AN=6;ExcessHet=0.4576	GT:GQ:RGQ	1/1:43:520	0/0:60	1/1:51:556
+chr20	199139	.	C	CTT	.	.	AC=1;AF=0.250;AN=4;ExcessHet=3.0103	GT:GQ:RGQ	0/1:9:151	0/0:40	./.
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/expected.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/expected.vcf.idx
new file mode 100644
index 00000000000..56e0c354ba6
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/expected.vcf.idx differ
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/sample_list b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/sample_list
new file mode 100644
index 00000000000..b71f627d551
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort/sample_list
@@ -0,0 +1,3 @@
+1,HG00405
+2,HG00408
+3,HG00418