Remove hardcoded limit on max homopolymer call

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AssemblyComplexity.java

@@ -4,6 +4,7 @@
 import htsjdk.samtools.util.Locatable;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
+import jdk.nashorn.internal.runtime.regexp.joni.constants.EncloseType;
 import org.apache.commons.lang.mutable.MutableInt;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.apache.commons.lang3.tuple.Triple;
@@ -81,8 +82,10 @@ public static Triple<int[], int[], double[]> annotate(final VariantContext vc,
         // with the greatest read support is considered germline, and as a heuristic we consider the second-most-supported
         // haplotype to be germline as well if it is at least half as supported (in terms of best read count) as the most-supported.
         // as above, we exclude differences at the variant site itself to avoid reference and germline bias
+        Comparator<Map.Entry<Haplotype,MutableInt>> countComparator = Comparator.comparingInt(entry -> -entry.getValue().intValue());
+        Comparator<Map.Entry<Haplotype,MutableInt>> alleleComparator =Comparator.comparing(entry -> entry.getKey().getBaseString());
         final List<Haplotype> haplotypesByDescendingSupport = haplotypeSupportCounts.entrySet().stream()
-                .sorted(Comparator.comparingInt(entry -> -entry.getValue().intValue()))
+                .sorted(countComparator.thenComparing(alleleComparator))
                 .map(entry -> entry.getKey())
                 .collect(Collectors.toList());
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java

@@ -337,7 +337,8 @@ public SWParameters getReadToHaplotypeSWParameters() {
 
     @Hidden
     @Advanced
-    @Argument(fullName=FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, doc="Collapse reference regions with >Nhmer during assembly, normal value when used is 12", optional = true)
+    @Argument(fullName=FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, doc="Collapse reference regions with >Nhmer during assembly, normal value when used is 12, " +
+            "-1 means - determine automatically from mc tag in the reads, 0 - disable", optional = true)
     public int flowAssemblyCollapseHKerSize = 0;
 
     @Advanced

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java

@@ -4,6 +4,7 @@
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileWriter;
+import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.variant.variantcontext.*;
@@ -52,6 +53,7 @@
 public final class AssemblyBasedCallerUtils {
 
     public static final int REFERENCE_PADDING_FOR_ASSEMBLY = 500;
+    public static final int DETERMINE_COLLAPSE_THRESHOLD = -1;
     public static final int NUM_HAPLOTYPES_TO_INJECT_FORCE_CALLING_ALLELES_INTO = 5;
     public static final String SUPPORTED_ALLELES_TAG="XA";
     public static final String CALLABLE_REGION_TAG = "CR";
@@ -363,8 +365,12 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
         final SWParameters haplotypeToReferenceSWParameters = argumentCollection.getHaplotypeToReferenceSWParameters();
 
         // establish reference mapper, if needed
-        final LongHomopolymerHaplotypeCollapsingEngine haplotypeCollapsing = (argumentCollection.flowAssemblyCollapseHKerSize > 0 && LongHomopolymerHaplotypeCollapsingEngine.needsCollapsing(refHaplotype.getBases(), argumentCollection.flowAssemblyCollapseHKerSize, logger))
-                                            ? new LongHomopolymerHaplotypeCollapsingEngine(argumentCollection.flowAssemblyCollapseHKerSize, argumentCollection.flowAssemblyCollapsePartialMode, fullReferenceWithPadding,
+        int collapseHmerSize = argumentCollection.flowAssemblyCollapseHKerSize;
+        if (collapseHmerSize == DETERMINE_COLLAPSE_THRESHOLD){
+            collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyColapseHmer(header);
+        }
+        final LongHomopolymerHaplotypeCollapsingEngine haplotypeCollapsing = ( collapseHmerSize > 0 && LongHomopolymerHaplotypeCollapsingEngine.needsCollapsing(refHaplotype.getBases(), collapseHmerSize, logger))
+                                            ? new LongHomopolymerHaplotypeCollapsingEngine(collapseHmerSize, argumentCollection.flowAssemblyCollapsePartialMode, fullReferenceWithPadding,
                 paddedReferenceLoc, logger, argumentCollection.assemblerArgs.debugAssembly, aligner, argumentCollection.getHaplotypeToReferenceSWParameters())
                                             : null;
         if ( haplotypeCollapsing != null ) {
@@ -411,6 +417,18 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
         }
     }
 
+    private static int determineFlowAssemblyColapseHmer(SAMFileHeader readsHeader) {
+        int result = 0;
+        List<SAMReadGroupRecord> rgr = readsHeader.getReadGroups();
+        for (SAMReadGroupRecord rg : rgr) {
+            FlowBasedReadUtils.ReadGroupInfo rgi = new FlowBasedReadUtils.ReadGroupInfo(rg);
+            if (rgi.maxClass >= result) {
+                result = rgi.maxClass;
+            }
+        }
+        return result;
+    }
+
     /**
      * Handle pileup detected alternate alleles.
      */
@@ -1217,4 +1235,5 @@ private static GATKRead revertSoftClippedBases(GATKRead inputRead){
         result.setAttribute(ReferenceConfidenceModel.ORIGINAL_SOFTCLIP_END_TAG, softEnd);
         return result;
     }
+
 }

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java

@@ -264,7 +264,7 @@ public enum FlowMode {
                 MIN_BASE_QUALITY_SCORE_SHORT_NAME, "0",
                 FILTER_ALLELES, "true",
                 FILTER_ALLELES_SOR_THRESHOLD, "3",
-                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, "12",
+                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, String.valueOf(AssemblyBasedCallerUtils.DETERMINE_COLLAPSE_THRESHOLD),
                 OVERRIDE_FRAGMENT_SOFTCLIP_CHECK_LONG_NAME, "true",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_PARALLEL_THREADS_LONG_NAME, "2",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_OPTIMIZED_COMP_LONG_NAME, "true",

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

@@ -475,7 +475,7 @@ public VCFHeader makeVCFHeader( final SAMSequenceDictionary sequenceDictionary,
         // where the filters are used.  For example, in emitting all sites the lowQual field is used
         headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
 
-        if ( hcArgs.flowAssemblyCollapseHKerSize > 0 ) {
+        if (( hcArgs.flowAssemblyCollapseHKerSize > 0 ) || (hcArgs.flowAssemblyCollapseHKerSize==AssemblyBasedCallerUtils.DETERMINE_COLLAPSE_THRESHOLD)){
             headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EXT_COLLAPSED_KEY));
         }
 

src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java

@@ -38,7 +38,7 @@
 
 public class FlowBasedRead extends SAMRecordToGATKReadAdapter implements GATKRead, Serializable {
 
-    final static public int     MAX_CLASS = 12;
+    public static final int  MAX_CLASS = 12; //note - this is a historical value to support files with max class is not defined in the header, it is expected that mc tag exists in the CRAM
     public static final String     DEFAULT_FLOW_ORDER = "TGCA";
     private static final long serialVersionUID = 42L;
     private final Logger logger = LogManager.getLogger(this.getClass());
@@ -224,7 +224,8 @@ public FlowBasedRead(final SAMRecord samRecord, final String flowOrder, final in
                 throw new GATKException("read missing flow matrix attribute: " + FLOW_MATRIX_TAG_NAME);
             }
         }
-        implementMatrixMods(FlowBasedReadUtils.getFlowMatrixModsInstructions(fbargs.flowMatrixMods));
+
+        implementMatrixMods(FlowBasedReadUtils.getFlowMatrixModsInstructions(fbargs.flowMatrixMods, maxHmer));
 
         //Spread boundary flow probabilities when the read is unclipped
         //in this case the value of the hmer is uncertain

src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java

@@ -29,7 +29,7 @@ static public class ReadGroupInfo {
 
         private String  reversedFlowOrder = null;
 
-        ReadGroupInfo(final SAMReadGroupRecord readGroup) {
+        public ReadGroupInfo(final SAMReadGroupRecord readGroup) {
 
             Utils.nonNull(readGroup);
             this.flowOrder = readGroup.getFlowOrder();
@@ -354,10 +354,10 @@ else if ( readEndMarkedUnclipped(gatkRead, mdArgs.FLOW_Q_IS_KNOWN_END) ) {
      *
      * For the implementation logic, see FlowBasedRead.fillFlowMatrix
      */
-    static public int[] getFlowMatrixModsInstructions(final String flowMatrixMods) {
+    static public int[] getFlowMatrixModsInstructions(final String flowMatrixMods, final int maxHmer) {
 
         if ( flowMatrixMods != null ) {
-            final int[] flowMatrixModsInstructions = new int[FlowBasedRead.MAX_CLASS + 1];
+            final int[] flowMatrixModsInstructions = new int[maxHmer + 1];
 
             final String[]    toks = flowMatrixMods.split(",");
             for ( int i = 0 ; i < toks.length - 1 ; i += 2 ) {

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -1771,6 +1771,7 @@ public void testGvcfWithAssemblyComplexityAnnotationRevamp() throws Exception {
                 .add("likelihood-calculation-engine","FlowBased")
                 .add("A", "AssemblyComplexity")
                 .addFlag("assembly-complexity-reference-mode")
+                .add("verbosity","INFO")
                 .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false);
 
         runCommandLine(args);

src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java

@@ -0,0 +1,32 @@
+package org.broadinstitute.hellbender.utils.read;
+import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMReadGroupRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.nio.file.FileSystems;
+import java.nio.file.Path;
+
+
+public class FlowBasedReadUtilsUnitTest extends GATKBaseTest{
+    @Test
+    void testReadGroupParsing() throws Exception{
+        final String    testResourceDir = publicTestDir + "org/broadinstitute/hellbender/utils/read/flow/reads/";
+        final String inputDir = testResourceDir + "/input/";
+
+        final Path inputFile = FileSystems.getDefault().getPath(inputDir, "sample_mc.bam");
+        final SamReader reader = SamReaderFactory.makeDefault().open(new File(inputFile.toString()));
+        SAMFileHeader header = reader.getFileHeader();
+        SAMReadGroupRecord rg1 = header.getReadGroup("UGAv3-72");
+        FlowBasedReadUtils.ReadGroupInfo frg1 = new FlowBasedReadUtils.ReadGroupInfo(rg1);
+        assert(frg1.maxClass==12);
+        assert(frg1.flowOrder.startsWith("TGCA"));
+        SAMReadGroupRecord rg2 = header.getReadGroup("UGAv3-73");
+        FlowBasedReadUtils.ReadGroupInfo frg2 = new FlowBasedReadUtils.ReadGroupInfo(rg2);
+        assert(frg2.maxClass==20);
+        assert(frg2.flowOrder.startsWith("TGCA"));
+    }
+}

src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf

@@ -3879,7 +3879,7 @@ chr9	81153765	.	G	<NON_REF>	.	.	END=81153766	GT:DP:GQ:MIN_DP:PL	0/0:27:69:25:0,6
 chr9	81153767	.	A	<NON_REF>	.	.	END=81153783	GT:DP:GQ:MIN_DP:PL	0/0:25:72:24:0,72,802
 chr9	81153784	.	A	<NON_REF>	.	.	END=81153785	GT:DP:GQ:MIN_DP:PL	0/0:28:22:27:0,22,996
 chr9	81153786	.	G	<NON_REF>	.	.	END=81153800	GT:DP:GQ:MIN_DP:PL	0/0:28:81:28:0,81,1175
-chr9	81153801	.	C	CA,<NON_REF>	0	.	ASSEMBLED_HAPS=10;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=90000.00|10800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=8,17|3,0|0,0;BaseQRankSum=0.000;DP=29;ExcessHet=0.0000;FILTERED_HAPS=6;HAPCOMP=4,0;HAPDOM=0.500,0.00;HEC=55,3,2,1,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.929;SUSP_NOISY_ADJACENT_TP_VARIANT	GT:AD:DP:GQ:PL:SB	0/0:25,3,0:28:18:0,18,58,75,692,115:8,17,3,0
+chr9	81153801	.	C	CA,<NON_REF>	0	.	ASSEMBLED_HAPS=10;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=90000.00|10800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=8,17|3,0|0,0;BaseQRankSum=0.000;DP=29;ExcessHet=0.0000;FILTERED_HAPS=6;HAPCOMP=0,0;HAPDOM=0.500,0.00;HEC=55,3,2,1,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=104400,29;ReadPosRankSum=0.929;SUSP_NOISY_ADJACENT_TP_VARIANT	GT:AD:DP:GQ:PL:SB	0/0:25,3,0:28:18:0,18,58,75,692,115:8,17,3,0
 chr9	81153802	.	T	<NON_REF>	.	.	END=81153833	GT:DP:GQ:MIN_DP:PL	0/0:38:99:34:0,99,1135
 chr9	81153834	.	C	<NON_REF>	.	.	END=81153834	GT:DP:GQ:MIN_DP:PL	0/0:39:23:39:0,23,1475
 chr9	81153835	.	A	<NON_REF>	.	.	END=81153835	GT:DP:GQ:MIN_DP:PL	0/0:39:83:39:0,83,1598
@@ -4206,7 +4206,7 @@ chr9	81156182	.	A	<NON_REF>	.	.	END=81156183	GT:DP:GQ:MIN_DP:PL	0/0:16:28:16:0,2
 chr9	81156184	.	A	<NON_REF>	.	.	END=81156185	GT:DP:GQ:MIN_DP:PL	0/0:15:13:13:0,13,144
 chr9	81156186	.	A	<NON_REF>	.	.	END=81156190	GT:DP:GQ:MIN_DP:PL	0/0:16:42:16:0,42,630
 chr9	81156191	.	T	<NON_REF>	.	.	END=81156194	GT:DP:GQ:MIN_DP:PL	0/0:15:36:15:0,36,540
-chr9	81156195	.	A	C,<NON_REF>	103.06	.	ASSEMBLED_HAPS=14;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|50400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,11|0,0;DP=15;ExcessHet=0.0000;FILTERED_HAPS=6;HAPCOMP=2,0;HAPDOM=0.250,0.00;HEC=10,6,5,2,1,1,1,0;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=54000,15	GT:AD:DP:GQ:PL:SB	1/1:0,14,0:14:42:117,42,0,595,42,117:0,0,3,11
+chr9	81156195	.	A	C,<NON_REF>	103.06	.	ASSEMBLED_HAPS=14;AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|50400.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|3,11|0,0;DP=15;ExcessHet=0.0000;FILTERED_HAPS=6;HAPCOMP=0,0;HAPDOM=0.250,0.00;HEC=10,6,5,2,1,1,1,0;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=54000,15	GT:AD:DP:GQ:PL:SB	1/1:0,14,0:14:42:117,42,0,595,42,117:0,0,3,11
 chr9	81156196	.	A	<NON_REF>	.	.	END=81156196	GT:DP:GQ:MIN_DP:PL	0/0:15:30:15:0,30,450
 chr9	81156197	.	T	<NON_REF>	.	.	END=81156197	GT:DP:GQ:MIN_DP:PL	0/0:15:10:15:0,10,592
 chr9	81156198	.	C	<NON_REF>	.	.	END=81156206	GT:DP:GQ:MIN_DP:PL	0/0:15:30:11:0,30,450
@@ -4408,7 +4408,7 @@ chr9	81158617	.	A	<NON_REF>	.	.	END=81158617	GT:DP:GQ:MIN_DP:PL	0/0:11:9:11:0,9,
 chr9	81158618	.	T	<NON_REF>	.	.	END=81158618	GT:DP:GQ:MIN_DP:PL	0/0:10:10:10:0,10,383
 chr9	81158619	.	G	<NON_REF>	.	.	END=81158621	GT:DP:GQ:MIN_DP:PL	0/0:9:27:9:0,27,377
 chr9	81158622	.	C	<NON_REF>	.	.	END=81158647	GT:DP:GQ:MIN_DP:PL	0/0:12:30:10:0,30,415
-chr9	81158648	.	G	GA,<NON_REF>	0.08	.	ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=32400.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=5,4|2,0|0,0;BaseQRankSum=0.000;DP=13;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=2,0;HAPDOM=0.500,0.00;HEC=11,7,6,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=46800,13;ReadPosRankSum=-0.447;SUSP_NOISY_ADJACENT_TP_VARIANT	GT:AD:DP:GQ:PL:SB	0/1:9,2,0:11:4:4,0,40,30,186,70:5,4,2,0
+chr9	81158648	.	G	GA,<NON_REF>	0.08	.	ASSEMBLED_HAPS=41;AS_RAW_BaseQRankSum=|0.0,1|NaN;AS_RAW_MQ=32400.00|7200.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=5,4|2,0|0,0;BaseQRankSum=0.000;DP=13;ExcessHet=0.0000;FILTERED_HAPS=28;HAPCOMP=1,0;HAPDOM=0.500,0.00;HEC=11,7,6,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=46800,13;ReadPosRankSum=-0.447;SUSP_NOISY_ADJACENT_TP_VARIANT	GT:AD:DP:GQ:PL:SB	0/1:9,2,0:11:4:4,0,40,30,186,70:5,4,2,0
 chr9	81158649	.	A	<NON_REF>	.	.	END=81158655	GT:DP:GQ:MIN_DP:PL	0/0:11:33:11:0,33,368
 chr9	81158656	.	A	<NON_REF>	.	.	END=81158656	GT:DP:GQ:MIN_DP:PL	0/0:12:21:12:0,21,461
 chr9	81158657	.	C	<NON_REF>	.	.	END=81158670	GT:DP:GQ:MIN_DP:PL	0/0:13:31:12:0,31,495

src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testVcfWithAssemblyComplexityAnnotation.expected.flowbased.vcf

@@ -3403,7 +3403,7 @@ chr9	81155350	.	CTAT	C	847.60	.	AC=1;AF=0.500;AN=2;ASSEMBLED_HAPS=12;BaseQRankSu
 chr9	81155468	.	A	AG	31.60	.	AC=1;AF=0.500;AN=2;ASSEMBLED_HAPS=4;BaseQRankSum=0.829;DP=32;ExcessHet=0.0000;FILTERED_HAPS=2;FS=31.854;HAPCOMP=0;HAPDOM=1.00;HEC=49,1;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=1.02;ReadPosRankSum=1.418;SOR=4.161	GT:AD:DP:GQ:PL	0/1:24,7:31:39:39,0,558
 chr9	81155738	.	A	C	616.06	.	AC=2;AF=1.00;AN=2;ASSEMBLED_HAPS=2;DP=15;ExcessHet=0.0000;FILTERED_HAPS=0;FS=0.000;HAPCOMP=0;HAPDOM=1.00;HEC=17;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.36;SOR=2.985	GT:AD:DP:GQ:PL	1/1:0,14:14:42:630,42,0
 chr9	81156114	.	G	T	459.64	.	AC=1;AF=0.500;AN=2;ASSEMBLED_HAPS=16;BaseQRankSum=1.862;DP=24;ExcessHet=0.0000;FILTERED_HAPS=12;FS=7.401;HAPCOMP=1;HAPDOM=0.462;HEC=7,6,6,6,1,0,0,0;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.15;ReadPosRankSum=0.435;SOR=2.546	GT:AD:DP:GQ:PL	0/1:11,13:24:99:467,0,422
-chr9	81156195	.	A	C	572.06	.	AC=2;AF=1.00;AN=2;ASSEMBLED_HAPS=16;DP=14;ExcessHet=0.0000;FILTERED_HAPS=12;FS=0.000;HAPCOMP=2;HAPDOM=0.357;HEC=11,11,2,1,1,0,0,0;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.73;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,14:14:42:586,42,0
+chr9	81156195	.	A	C	572.06	.	AC=2;AF=1.00;AN=2;ASSEMBLED_HAPS=16;DP=14;ExcessHet=0.0000;FILTERED_HAPS=12;FS=0.000;HAPCOMP=0;HAPDOM=0.357;HEC=11,11,2,1,1,0,0,0;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.73;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,14:14:42:586,42,0
 chr9	81156491	.	T	TA	42.92	.	AC=2;AF=1.00;AN=2;ASSEMBLED_HAPS=4;DP=23;ExcessHet=0.0000;FILTERED_HAPS=2;FS=0.000;HAPCOMP=0;HAPDOM=0.571;HEC=39,3;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=7.15;SOR=1.329;SUSP_NOISY_ADJACENT_TP_VARIANT	GT:AD:DP:GQ:PL	1/1:0,6:6:15:57,15,0
 chr9	81158690	.	C	CT	404.03	.	AC=2;AF=1.00;AN=2;ASSEMBLED_HAPS=32;DP=15;ExcessHet=0.0000;FILTERED_HAPS=28;FS=0.000;HAPCOMP=1;HAPDOM=0.500;HEC=17,7,2,2,1,1,0,0,0,0,0,0,0,0,0,0;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.86;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,14:14:42:418,42,0
 chr9	81158712	.	A	G	293.64	.	AC=1;AF=0.500;AN=2;ASSEMBLED_HAPS=32;BaseQRankSum=0.728;DP=15;ExcessHet=0.0000;FILTERED_HAPS=28;FS=5.497;HAPCOMP=1;HAPDOM=0.875;HEC=13,11,2,2,1,1,0,0,0,0,0,0,0,0,0,0;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=19.58;ReadPosRankSum=-0.675;SOR=0.078	GT:AD:DP:GQ:PL	0/1:7,8:15:99:301,0,256