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Remove hardcoded limit on max homopolymer call (#8088)
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* Fixing hard coded max hmer in flow matrix mods
* Added comment regarding MAX_CLASS
* Make code determine the collapsing automatically
* Fixed a bug in assembly complexity annotation that caused difference in results between JAVA8 and JAVA11
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@ilyasoifer
ilyasoifer authored Dec 7, 2022
1 parent 894117c commit 84ade40
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Showing 14 changed files with 72 additions and 15 deletions.
5 changes: 4 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AssemblyComplexity.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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());

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3 changes: 2 additions & 1 deletion ...itute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
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Expand Up @@ -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
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23 changes: 21 additions & 2 deletions ...org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java
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Expand Up @@ -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.*;
Expand Down Expand Up @@ -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";
Expand Down Expand Up @@ -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 ) {
Expand Down Expand Up @@ -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.
*/
Expand Down Expand Up @@ -1217,4 +1235,5 @@ private static GATKRead revertSoftClippedBases(GATKRead inputRead){
result.setAttribute(ReferenceConfidenceModel.ORIGINAL_SOFTCLIP_END_TAG, softEnd);
return result;
}

}
2 changes: 1 addition & 1 deletion ...institute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
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Expand Up @@ -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",
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2 changes: 1 addition & 1 deletion ...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
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Expand Up @@ -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));
}

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5 changes: 3 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedRead.java
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Expand Up @@ -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());
Expand Down Expand Up @@ -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
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java
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Expand Up @@ -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();
Expand Down Expand Up @@ -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 ) {
Expand Down
1 change: 1 addition & 0 deletions ...oadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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Expand Up @@ -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);
Expand Down
32 changes: 32 additions & 0 deletions src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java
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@@ -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"));
}
}
6 changes: 3 additions & 3 deletions ...ols/haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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Binary file modified ...haplotypecaller/testGvcfWithAssemblyComplexityAnnotationRevamp.expected.flowbased.vcf.idx
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2 changes: 1 addition & 1 deletion ...nder/tools/haplotypecaller/testVcfWithAssemblyComplexityAnnotation.expected.flowbased.vcf
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Expand Up @@ -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
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