diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java index 6363ec1d914..6e60578b026 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java @@ -166,8 +166,7 @@ private static List replaceWithNoCallsAndDels(final VariantContext vc) { * @return never {@code null} */ //TODO as part of a larger refactoring effort {@link #remapAlleles} can be merged with {@link GATKVariantContextUtils#remapAlleles}. - @VisibleForTesting - static List remapAlleles(final VariantContext vc, final Allele refAllele) { + public static List remapAlleles(final VariantContext vc, final Allele refAllele) { final Allele vcRef = vc.getReference(); final byte[] refBases = refAllele.getBases(); final int extraBaseCount = refBases.length - vcRef.getBases().length; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java index 0b5143d48a1..d4408f43367 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java @@ -79,8 +79,16 @@ public static GenotypesContext subsetAlleles(final GenotypesContext originalGs, } final boolean useNewLikelihoods = newLikelihoods != null && (depth != 0 || GATKVariantContextUtils.isInformative(newLikelihoods)); - final GenotypeBuilder gb = useNewLikelihoods ? new GenotypeBuilder(g).PL(newLikelihoods).log10PError(newLog10GQ) : new GenotypeBuilder(g).noPL().noGQ(); - + final GenotypeBuilder gb = new GenotypeBuilder(g); + if (useNewLikelihoods) { + final Map attributes = new HashMap<>(g.getExtendedAttributes()); + gb.PL(newLikelihoods).log10PError(newLog10GQ); + attributes.remove(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY); + gb.noAttributes().attributes(attributes); + } + else { + gb.noPL().noGQ(); + } GATKVariantContextUtils.makeGenotypeCall(g.getPloidy(), gb, assignmentMethod, newLikelihoods, allelesToKeep); // restrict SAC to the new allele subset diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java index 92f8dd1d38f..ccfcdf83576 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java @@ -1,7 +1,10 @@ package org.broadinstitute.hellbender.tools.walkers.genotyper; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.argparser.Advanced; import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.hellbender.engine.FeatureInput; +import org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; @@ -13,6 +16,10 @@ public final class GenotypeCalculationArgumentCollection implements Serializable { private static final long serialVersionUID = 1L; + public static final String SUPPORTING_CALLSET_LONG_NAME = "population-callset"; + public static final String SUPPORTING_CALLSET_SHORT_NAME = "population"; + public static final String NUM_REF_SAMPLES_LONG_NAME = "num-reference-samples-if-no-call"; + /** * Creates a GenotypeCalculationArgumentCollection with default values. */ @@ -34,6 +41,8 @@ public GenotypeCalculationArgumentCollection( final GenotypeCalculationArgumentC this.MAX_ALTERNATE_ALLELES = other.MAX_ALTERNATE_ALLELES; this.inputPrior = new ArrayList<>(other.inputPrior); this.samplePloidy = other.samplePloidy; + this.supportVariants = other.supportVariants; + this.numRefIfMissing = other.numRefIfMissing; } /** @@ -90,7 +99,7 @@ public GenotypeCalculationArgumentCollection( final GenotypeCalculationArgumentC * The standard deviation of the distribution of alt allele fractions. The above heterozygosity parameters give the * *mean* of this distribution; this parameter gives its spread. */ - @Argument(fullName = "heterozygosity-stdev", doc = "Standard deviation of eterozygosity for SNP and indel calling.", optional = true) + @Argument(fullName = "heterozygosity-stdev", doc = "Standard deviation of heterozygosity for SNP and indel calling.", optional = true) public double heterozygosityStandardDeviation = 0.01; /** @@ -165,4 +174,20 @@ public GenotypeCalculationArgumentCollection( final GenotypeCalculationArgumentC */ @Argument(shortName="ploidy", fullName="sample-ploidy", doc="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).", optional=true) public int samplePloidy = HomoSapiensConstants.DEFAULT_PLOIDY; + + /** + * Supporting external panel. Allele counts from this panel (taken from AC,AN or MLEAC,AN or raw genotypes) will + * be used to inform the frequency distribution underlying the genotype priors. These files must be VCF 4.2 spec or later. + * Note that unlike CalculateGenotypePosteriors, HaplotypeCaller only allows one supporting callset. + */ + @Argument(fullName=SUPPORTING_CALLSET_LONG_NAME, shortName=SUPPORTING_CALLSET_SHORT_NAME, doc="Callset to use in calculating genotype priors", optional=true) + public FeatureInput supportVariants = null; + + /** + * When a variant is not seen in any panel, this argument controls whether to infer (and with what effective strength) + * that only reference alleles were observed at that site. E.g. "If not seen in 1000Genomes, treat it as AC=0, + * AN=2000". + */ + @Argument(fullName= NUM_REF_SAMPLES_LONG_NAME,doc="Number of hom-ref genotypes to infer at sites not present in a panel",optional=true) + public int numRefIfMissing = 0; } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java index f6851be7b39..3fb39128249 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -2,6 +2,7 @@ import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.barclay.argparser.Argument; import org.broadinstitute.barclay.argparser.ArgumentCollection; @@ -18,6 +19,10 @@ import org.broadinstitute.hellbender.utils.io.IOUtils; import java.io.FileNotFoundException; +import java.util.ArrayList; +import java.util.List; +import org.broadinstitute.hellbender.utils.io.IOUtils; +import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import java.nio.file.Path; import java.util.List; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java index f7703b997cf..1ec3d851554 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java @@ -178,7 +178,7 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5 genotypingEngine = new HaplotypeCallerGenotypingEngine(hcArgs, samplesList, FixedAFCalculatorProvider.createThreadSafeProvider(hcArgs), ! hcArgs.doNotRunPhysicalPhasing); genotypingEngine.setAnnotationEngine(annotationEngine); - referenceConfidenceModel = new ReferenceConfidenceModel(samplesList, readsHeader, hcArgs.indelSizeToEliminateInRefModel); + referenceConfidenceModel = new ReferenceConfidenceModel(samplesList, readsHeader, hcArgs.indelSizeToEliminateInRefModel, hcArgs.genotypeArgs.numRefIfMissing); //Allele-specific annotations are not yet supported in the VCF mode if (isAlleleSpecificMode(annotationEngine) && isVCFMode()){ @@ -373,6 +373,14 @@ public VCFHeader makeVCFHeader( final SAMSequenceDictionary sequenceDictionary, VCFConstants.DEPTH_KEY, VCFConstants.GENOTYPE_PL_KEY); + if (hcArgs.genotypeArgs.supportVariants != null) { + headerInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY)); + headerInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY)); + headerInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY)); + headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.GENOTYPE_PRIOR_KEY)); + } + if ( ! hcArgs.doNotRunPhysicalPhasing ) { headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY)); headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY)); @@ -481,13 +489,18 @@ public List callRegion(final AssemblyRegion region, final Featur return NO_CALLS; } + final List VCpriors = new ArrayList<>(); + if (hcArgs.genotypeArgs.supportVariants != null) { + features.getValues(hcArgs.genotypeArgs.supportVariants).stream().forEach(VCpriors::add); + } + if ( hcArgs.sampleNameToUse != null ) { removeReadsFromAllSamplesExcept(hcArgs.sampleNameToUse, region); } if( ! region.isActive() ) { // Not active so nothing to do! - return referenceModelForNoVariation(region, true); + return referenceModelForNoVariation(region, true, VCpriors); } final List givenAlleles = new ArrayList<>(); @@ -496,11 +509,11 @@ public List callRegion(final AssemblyRegion region, final Featur // No alleles found in this region so nothing to do! if ( givenAlleles.isEmpty() ) { - return referenceModelForNoVariation(region, true); + return referenceModelForNoVariation(region, true, VCpriors); } } else if( region.size() == 0 ) { // No reads here so nothing to do! - return referenceModelForNoVariation(region, true); + return referenceModelForNoVariation(region, true, VCpriors); } // run the local assembler, getting back a collection of information on how we should proceed @@ -514,7 +527,7 @@ public List callRegion(final AssemblyRegion region, final Featur final AssemblyRegionTrimmer.Result trimmingResult = trimmer.trim(region, allVariationEvents); if ( ! trimmingResult.isVariationPresent() && ! hcArgs.disableOptimizations ) { - return referenceModelForNoVariation(region, false); + return referenceModelForNoVariation(region, false, VCpriors); } final AssemblyResultSet assemblyResult = @@ -533,7 +546,7 @@ public List callRegion(final AssemblyRegion region, final Featur // abort early if something is out of the acceptable range // TODO is this ever true at this point??? perhaps GGA. Need to check. if( ! assemblyResult.isVariationPresent() && ! hcArgs.disableOptimizations ) { - return referenceModelForNoVariation(region, false); + return referenceModelForNoVariation(region, false, VCpriors); } // For sure this is not true if gVCF is on. @@ -544,7 +557,7 @@ public List callRegion(final AssemblyRegion region, final Featur // TODO is this ever true at this point??? perhaps GGA. Need to check. if ( regionForGenotyping.size() == 0 && ! hcArgs.disableOptimizations ) { // no reads remain after filtering so nothing else to do! - return referenceModelForNoVariation(region, false); + return referenceModelForNoVariation(region, false, VCpriors); } // evaluate each sample's reads against all haplotypes @@ -594,21 +607,22 @@ public List callRegion(final AssemblyRegion region, final Featur if ( emitReferenceConfidence() ) { if ( !containsCalls(calledHaplotypes) ) { // no called all of the potential haplotypes - return referenceModelForNoVariation(region, false); + return referenceModelForNoVariation(region, false, VCpriors); } else { final List result = new LinkedList<>(); // output left-flanking non-variant section: if (trimmingResult.hasLeftFlankingRegion()) { - result.addAll(referenceModelForNoVariation(trimmingResult.nonVariantLeftFlankRegion(), false)); + result.addAll(referenceModelForNoVariation(trimmingResult.nonVariantLeftFlankRegion(), false, VCpriors)); } // output variant containing region. result.addAll(referenceConfidenceModel.calculateRefConfidence(assemblyResult.getReferenceHaplotype(), calledHaplotypes.getCalledHaplotypes(), assemblyResult.getPaddedReferenceLoc(), regionForGenotyping, - readLikelihoods, genotypingEngine.getPloidyModel(), calledHaplotypes.getCalls())); + readLikelihoods, genotypingEngine.getPloidyModel(), calledHaplotypes.getCalls(), hcArgs.genotypeArgs.supportVariants != null, + VCpriors)); // output right-flanking non-variant section: if (trimmingResult.hasRightFlankingRegion()) { - result.addAll(referenceModelForNoVariation(trimmingResult.nonVariantRightFlankRegion(), false)); + result.addAll(referenceModelForNoVariation(trimmingResult.nonVariantRightFlankRegion(), false, VCpriors)); } return result; } @@ -636,7 +650,7 @@ private boolean containsCalls(final HaplotypeCallerGenotypingEngine.CalledHaplot * @param needsToBeFinalized should the region be finalized before computing the ref model (should be false if already done) * @return a list of variant contexts (can be empty) to emit for this ref region */ - private List referenceModelForNoVariation(final AssemblyRegion region, final boolean needsToBeFinalized) { + private List referenceModelForNoVariation(final AssemblyRegion region, final boolean needsToBeFinalized, final List VCpriors) { if ( emitReferenceConfidence() ) { //TODO - why the activeRegion cannot manage its own one-time finalization and filtering? //TODO - perhaps we can remove the last parameter of this method and the three lines bellow? @@ -650,7 +664,7 @@ private List referenceModelForNoVariation(final AssemblyRegion r final List haplotypes = Collections.singletonList(refHaplotype); return referenceConfidenceModel.calculateRefConfidence(refHaplotype, haplotypes, paddedLoc, region, createDummyStratifiedReadMap(refHaplotype, samplesList, region), - genotypingEngine.getPloidyModel(), Collections.emptyList()); + genotypingEngine.getPloidyModel(), Collections.emptyList(), hcArgs.genotypeArgs.supportVariants != null, VCpriors); } else { return NO_CALLS; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index 2cd88646136..30835d1cba5 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -39,6 +39,8 @@ public class HaplotypeCallerGenotypingEngine extends AssemblyBasedCallerGenotypi private final PloidyModel ploidyModel; private final ReferenceConfidenceMode referenceConfidenceMode; + protected final double snpHeterozygosity; + protected final double indelHeterozygosity; private final int maxGenotypeCountToEnumerate; private final Map practicalAlleleCountForPloidy = new HashMap<>(); @@ -56,6 +58,8 @@ public HaplotypeCallerGenotypingEngine(final HaplotypeCallerArgumentCollection c genotypingModel = new IndependentSampleGenotypesModel(); maxGenotypeCountToEnumerate = configuration.genotypeArgs.MAX_GENOTYPE_COUNT; referenceConfidenceMode = configuration.emitReferenceConfidence; + snpHeterozygosity = configuration.genotypeArgs.snpHeterozygosity; + indelHeterozygosity = configuration.genotypeArgs.indelHeterozygosity; } @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index c253a864a95..ecc6f03e940 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -12,6 +12,7 @@ import org.broadinstitute.hellbender.engine.AlignmentContext; import org.broadinstitute.hellbender.engine.AssemblyRegion; import org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel; +import org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils; import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; @@ -27,8 +28,10 @@ import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import java.util.*; +import java.util.stream.Collectors; import java.util.stream.DoubleStream; /** @@ -42,6 +45,9 @@ public final class ReferenceConfidenceModel { private final SampleList samples; private final int indelInformativeDepthIndelSize; + private final int numRefSamplesForPrior; + + private final PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions options; /** * Surrogate quality score for no base calls. @@ -91,6 +97,15 @@ public final class ReferenceConfidenceModel { private static final double INDEL_LIKELIHOOD = QualityUtils.qualToErrorProbLog10(INDEL_QUAL); private static final int IDX_HOM_REF = 0; + /** + * Options related to posterior probability calcs + */ + private static final boolean useInputSamplesAlleleCounts = false; //by definition ref-conf will be single-sample; inputs should get ignored but let's be explicit + private static final boolean useMLEAC = true; + private static final boolean ignoreInputSamplesForMissingVariants = true; + private static final boolean useFlatPriorsForIndels = false; + + /** * Holds information about a genotype call of a single sample reference vs. any non-ref event * @@ -156,7 +171,8 @@ int[] getAD() { */ public ReferenceConfidenceModel(final SampleList samples, final SAMFileHeader header, - final int indelInformativeDepthIndelSize) { + final int indelInformativeDepthIndelSize, + final int numRefForPrior) { Utils.nonNull(samples, "samples cannot be null"); Utils.validateArg( samples.numberOfSamples() > 0, "samples cannot be empty"); Utils.nonNull(header, "header cannot be empty"); @@ -165,6 +181,10 @@ public ReferenceConfidenceModel(final SampleList samples, this.samples = samples; this.indelInformativeDepthIndelSize = indelInformativeDepthIndelSize; + this.numRefSamplesForPrior = numRefForPrior; + this.options = new PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions(HomoSapiensConstants.SNP_HETEROZYGOSITY, + HomoSapiensConstants.INDEL_HETEROZYGOSITY, useInputSamplesAlleleCounts, useMLEAC, ignoreInputSamplesForMissingVariants, + useFlatPriorsForIndels); } /** @@ -177,6 +197,17 @@ public Set getVCFHeaderLines() { return headerLines; } + public List calculateRefConfidence(final Haplotype refHaplotype, + final Collection calledHaplotypes, + final SimpleInterval paddedReferenceLoc, + final AssemblyRegion activeRegion, + final ReadLikelihoods readLikelihoods, + final PloidyModel ploidyModel, + final List variantCalls) { + return calculateRefConfidence(refHaplotype, calledHaplotypes, paddedReferenceLoc, activeRegion, readLikelihoods, + ploidyModel, variantCalls, false, Collections.emptyList()); + } + /** * Calculate the reference confidence for a single sample given the its read data * @@ -204,7 +235,9 @@ public List calculateRefConfidence(final Haplotype refHaplotype, final AssemblyRegion activeRegion, final ReadLikelihoods readLikelihoods, final PloidyModel ploidyModel, - final List variantCalls) { + final List variantCalls, + final boolean applyPriors, + final List VCpriors) { Utils.nonNull(refHaplotype, "refHaplotype cannot be null"); Utils.nonNull(calledHaplotypes, "calledHaplotypes cannot be null"); Utils.validateArg(calledHaplotypes.contains(refHaplotype), "calledHaplotypes must contain the refHaplotype"); @@ -228,24 +261,34 @@ public List calculateRefConfidence(final Haplotype refHaplotype, final int offset = curPos.getStart() - refSpan.getStart(); final VariantContext overlappingSite = getOverlappingVariantContext(curPos, variantCalls); + final List currentPriors = getMatchingPriors(curPos, overlappingSite, VCpriors); if ( overlappingSite != null && overlappingSite.getStart() == curPos.getStart() ) { - results.add(overlappingSite); + if (applyPriors) { + results.add(PosteriorProbabilitiesUtils.calculatePosteriorProbs(overlappingSite, currentPriors, + numRefSamplesForPrior, options)); + } + else { + results.add(overlappingSite); + } } else { // otherwise emit a reference confidence variant context - results.add(makeReferenceConfidenceVariantContext(ploidy, ref, sampleName, globalRefOffset, pileup, curPos, offset)); + results.add(makeReferenceConfidenceVariantContext(ploidy, ref, sampleName, globalRefOffset, pileup, curPos, offset, applyPriors, currentPriors)); } } return results; } - private VariantContext makeReferenceConfidenceVariantContext(final int ploidy, + + private VariantContext makeReferenceConfidenceVariantContext(final int ploidy, final byte[] ref, final String sampleName, final int globalRefOffset, final ReadPileup pileup, final Locatable curPos, - final int offset) { + final int offset, + final boolean applyPriors, + final List VCpriors) { // Assume infinite population on a single sample. final int refOffset = offset + globalRefOffset; final byte refBase = ref[refOffset]; @@ -275,8 +318,13 @@ private VariantContext makeReferenceConfidenceVariantContext(final int ploidy, gb.GQ(GATKVariantContextUtils.calculateGQFromPLs(leastConfidenceGLsAsPLs)); gb.PL(leastConfidenceGLsAsPLs); - vcb.genotypes(gb.make()); - return vcb.make(); + if(!applyPriors) { + return vcb.genotypes(gb.make()).make(); + } + else { + return PosteriorProbabilitiesUtils.calculatePosteriorProbs(vcb.genotypes(gb.make()).make(), VCpriors, numRefSamplesForPrior, options); + //TODO FIXME: after new-qual refactoring, these should be static calls to AF calculator + } } /** @@ -462,6 +510,18 @@ VariantContext getOverlappingVariantContext(final Locatable curPos, final Collec return overlaps; } + /** + * Note that we don't have to match alleles because the PosteriorProbabilitesUtils will take care of that + * @param curPos position of interest for genotyping + * @param call (may be null) + * @param priorList priors within the current ActiveRegion + * @return prior VCs representing the same variant position as call + */ + List getMatchingPriors(final Locatable curPos, final VariantContext call, final List priorList) { + final int position = call != null ? call.getStart() : curPos.getStart(); + return priorList.stream().filter(vc -> position == vc.getStart()).collect(Collectors.toList()); + } + /** * Compute the sum of mismatching base qualities for readBases aligned to refBases at readStart / refStart * assuming no insertions or deletions in the read w.r.t. the reference diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java index caee971c890..9e414ff6f92 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java @@ -4,9 +4,7 @@ import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.VariantContextUtils; -import htsjdk.variant.variantcontext.writer.Options; import htsjdk.variant.variantcontext.writer.VariantContextWriter; -import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder; import htsjdk.variant.vcf.*; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; @@ -22,6 +20,7 @@ import java.io.File; import java.util.*; +import java.util.stream.Collectors; /** * Calculate genotype posterior probabilities given family and/or known population genotypes @@ -142,27 +141,36 @@ public final class CalculateGenotypePosteriors extends VariantWalker { private static final Logger logger = LogManager.getLogger(CalculateGenotypePosteriors.class); + public static final String SUPPORTING_CALLSETS_SHORT_NAME = "supporting"; + public static final String SUPPORTING_CALLSETS_LONG_NAME = "supporting-callsets"; + public static final String NUM_REF_SAMPLES_LONG_NAME = "num-reference-samples-if-no-call"; + /** * Supporting external panels. Allele counts from these panels (taken from AC,AN or MLEAC,AN or raw genotypes) will * be used to inform the frequency distribution underlying the genotype priors. These files must be VCF 4.2 spec or later. */ - @Argument(fullName="supporting-callsets", shortName = "supporting", doc="Other callsets to use in generating genotype posteriors", optional=true) + @Argument(fullName=SUPPORTING_CALLSETS_LONG_NAME, shortName = SUPPORTING_CALLSETS_SHORT_NAME, doc="Other callsets to use in generating genotype posteriors", optional=true) public List> supportVariants = new ArrayList<>(); @Argument(doc="File to which variants should be written", fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, optional = false) public File out = null; /** - * The global prior of a variant site -- i.e. the expected allele frequency distribution knowing only that N alleles - * exist, and having observed none of them. This is the "typical" 1/x trend, modeled here as not varying - * across alleles. The calculation for this parameter is (Effective population size) * (steady state mutation rate) - * + * Prior SNP pseudocounts for Dirichlet distribution of allele frequencies. The posterior distribution is a + * Dirichlet with parameters given by pseudocounts plus the number of occurrences in the resource vcfs. + */ + @Argument(fullName="global-prior-snp", doc="Global Dirichlet prior parameters for the SNP allele frequency",optional=true) + public double globalPriorSnp = HomoSapiensConstants.SNP_HETEROZYGOSITY; + + /** + * Prior indel pseudocounts for Dirichlet distribution of allele frequencies. The posterior distribution is a + * Dirichlet with parameters given by pseudocounts plus the number of occurrences in the resource vcfs. */ - @Argument(fullName="global-prior", doc="Global Dirichlet prior parameters for the allele frequency",optional=true) - public double globalPrior = HomoSapiensConstants.SNP_HETEROZYGOSITY; + @Argument(fullName="global-prior-indel", doc="Global Dirichlet prior parameters for the indel allele frequency",optional=true) + public double globalPriorIndel = HomoSapiensConstants.SNP_HETEROZYGOSITY; /** - * The mutation prior -- i.e. the probability that a new mutation occurs. Sensitivity analysis on known de novo + * The de novo mutation prior -- i.e. the probability that a new mutation occurs. Sensitivity analysis on known de novo * mutations suggests a default value of 10^-6. * */ @@ -172,10 +180,9 @@ public final class CalculateGenotypePosteriors extends VariantWalker { /** * When a variant is not seen in a panel, this argument controls whether to infer (and with what effective strength) * that only reference alleles were observed at that site. E.g. "If not seen in 1000Genomes, treat it as AC=0, - * AN=2000". This is applied across all external panels, so if numRefIsMissing = 10, and the variant is absent in - * two panels, this confers evidence of AC=0,AN=20. + * AN=2000", where AN=2*nSamples for human autosomes. */ - @Argument(fullName="num-reference-samples-if-no-call",doc="Number of hom-ref genotypes to infer at sites not present in a panel",optional=true) + @Argument(fullName=NUM_REF_SAMPLES_LONG_NAME,doc="Number of hom-ref genotypes to infer at sites not present in a panel",optional=true) public int numRefIfMissing = 0; /** @@ -195,11 +202,20 @@ public final class CalculateGenotypePosteriors extends VariantWalker { public boolean ignoreInputSamples = false; /** - * Calculate priors for missing external variants from sample data -- default behavior is to apply flat priors + * Don't add input sample ACs for variants not seen in the supporting panel. Default is to add discovered AC from input samples + * provided there are at least 10 input samples or if num-ref-samples-if-no-call is greater than zero. */ @Argument(fullName="discovered-allele-count-priors-off",doc="Do not use discovered allele count in the input callset " + "for variants that do not appear in the external callset. ", optional=true) - public boolean useACoff = false; + public boolean ignoreInputSamplesForMissingResources = false; + + /** + * Use flat priors for indels (can be used to replicate the legacy CalculateGenotypePosteriors behavior) + * If an input variant contains an indel allele, flat priors will be applied to that site. If a reference panel + * variant contains an indel allele, flat priors will be applied instead. + */ + @Argument(fullName = "use-flat-priors-for-indels", shortName = "skipIndels", doc="Use flat priors for indels") + public boolean useFlatPriorsForIndels = false; /** * Skip application of population-based priors @@ -226,6 +242,8 @@ public final class CalculateGenotypePosteriors extends VariantWalker { private VariantContextWriter vcfWriter; + private PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions options; + @Override public void onTraversalStart() { vcfWriter = createVCFWriter(out); @@ -278,6 +296,9 @@ public void onTraversalStart() { final Map> families = sampleDB.getFamilies(vcfSamples); famUtils = new FamilyLikelihoods(sampleDB, deNovoPrior, vcfSamples, families); + + options = new PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions(globalPriorSnp, globalPriorIndel, + !ignoreInputSamples, !defaultToAC, ignoreInputSamplesForMissingResources, useFlatPriorsForIndels); } /** @@ -299,7 +320,9 @@ public void apply(final VariantContext variant, final Collection otherVCs = featureContext.getValues(supportVariants); - final int missing = supportVariants.size() - otherVCs.size(); + //If no resource contains a matching variant, then add numRefIfMissing as a pseudocount to the priors + List resourcesWithMatchingStarts = otherVCs.stream() + .filter(vc -> variant.getStart() == vc.getStart()).collect(Collectors.toList()); //do family priors first (if applicable) final VariantContextBuilder builder = new VariantContextBuilder(variant); @@ -313,7 +336,8 @@ public void apply(final VariantContext variant, final VariantContext vc_bothPriors; if (!skipPopulationPriors) { - vc_bothPriors = PosteriorProbabilitiesUtils.calculatePosteriorProbs(vc_familyPriors, otherVCs, missing * numRefIfMissing, globalPrior, !ignoreInputSamples, defaultToAC, useACoff); + vc_bothPriors = PosteriorProbabilitiesUtils.calculatePosteriorProbs(vc_familyPriors, resourcesWithMatchingStarts, + resourcesWithMatchingStarts.isEmpty() ? numRefIfMissing : 0, options); } else { vc_bothPriors = vc_familyPriors; } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtils.java index d33d4fc5634..ac2a287581c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtils.java @@ -3,66 +3,137 @@ import com.google.common.annotations.VisibleForTesting; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; +import org.apache.commons.collections.ListUtils; import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger; import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod; import org.broadinstitute.hellbender.utils.MathUtils; +import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import java.util.*; import java.util.stream.Collectors; public final class PosteriorProbabilitiesUtils { + final private static int minSamplesToUseInputs = 10; private PosteriorProbabilitiesUtils(){} /** - * Calculates phred-scaled posterior probabilities for genotypes given the data and allele frequency priors. + * A class to wrangle all the various and sundry genotype posterior options, + * mostly from CalculateGenotypePosteriors */ + public final static class PosteriorProbabilitiesOptions { + double snpPriorDirichlet; + double indelPriorDirichlet; + boolean useInputSamplesAlleleCounts; + boolean useMLEAC; + boolean ignoreInputSamplesForMissingResources; + boolean useFlatPriorsForIndels; + + public PosteriorProbabilitiesOptions(final double snpPriorDirichlet, + final double indelPriorDirichlet, + final boolean useInputSamplesAlleleCounts, + final boolean useMLEAC, + final boolean ignoreInputSamplesForMissingResources, + final boolean useFlatPriorsForIndels) { + this.snpPriorDirichlet = snpPriorDirichlet; + this.indelPriorDirichlet = indelPriorDirichlet; + this.useInputSamplesAlleleCounts = useInputSamplesAlleleCounts; + this.useMLEAC = useMLEAC; + this.ignoreInputSamplesForMissingResources = ignoreInputSamplesForMissingResources; + this.useFlatPriorsForIndels = useFlatPriorsForIndels; + } + } + + /** + * Calculates phred-scaled posterior probabilities for genotypes given the data and allele frequency priors. + * + * @param vc1 input variant context + * @param resources variants to use to calculate genotype priors (should already be checked for matching start position) + * @param numRefSamplesFromMissingResources the number of reference samples to use for the prior (already accounted for resource missingness) + * @return a VariantContext with PLs and PPs in the genotypes and a PG tag for the Phred-scaled prior in the INFO field if + */ public static VariantContext calculatePosteriorProbs(final VariantContext vc1, - final Collection resources, + final List resources, final int numRefSamplesFromMissingResources, - final double globalFrequencyPriorDirichlet, - final boolean useInputSamples, - final boolean useAC, - final boolean useACoff) { + final PosteriorProbabilitiesOptions opts) { Utils.nonNull(vc1, "VariantContext vc1 is null"); final Map totalAlleleCounts = new HashMap<>(); - //only use discovered allele count if there are at least 10 samples - final boolean useDiscoveredAC = !useACoff && vc1.getNSamples() >= 10; - if(vc1.isSNP()) { - //store the allele counts for each allele in the variant priors - resources.forEach(r -> addAlleleCounts(totalAlleleCounts, r, useAC)); + //only use discovered allele count for missing resources if there are at least 10 samples or if we have reference samples + final boolean useDiscoveredACForMissing = !opts.ignoreInputSamplesForMissingResources && (vc1.getNSamples() >= minSamplesToUseInputs || numRefSamplesFromMissingResources != 0); + + //deletions introduce ref allele padding issues + @SuppressWarnings("unchecked") + List allAlleles = ListUtils.union(resources, Arrays.asList(vc1)); + final Allele commonRef = GATKVariantContextUtils.determineReferenceAllele(allAlleles, new SimpleInterval(vc1)); + final List origAllelesRemapped = ReferenceConfidenceVariantContextMerger.remapAlleles(vc1, commonRef); - //add the allele counts from the input samples (if applicable) - if ( useInputSamples ) { - addAlleleCounts(totalAlleleCounts,vc1,useAC); + + final int referenceAlleleCountForMissing = resources.isEmpty() ? HomoSapiensConstants.DEFAULT_PLOIDY*numRefSamplesFromMissingResources : 0; //because we're dealing with diploids + //store the allele counts for each allele in the variant priors + for (final VariantContext r : resources) { + if (r.getStart() == vc1.getStart()) { + final List remappedAlleles = ReferenceConfidenceVariantContextMerger.remapAlleles(r, commonRef); + addAlleleCounts(totalAlleleCounts, r, remappedAlleles, !opts.useMLEAC); } + } + + //add the allele counts from the input samples (if applicable) + if ( (opts.useInputSamplesAlleleCounts && !resources.isEmpty()) || (resources.isEmpty() && useDiscoveredACForMissing)) { + addAlleleCounts(totalAlleleCounts,vc1,origAllelesRemapped, !opts.useMLEAC); + } + + //add zero allele counts for any reference alleles not seen in priors (if applicable) + final int existingRefCounts = totalAlleleCounts.getOrDefault(commonRef, 0); + totalAlleleCounts.put(commonRef, existingRefCounts + referenceAlleleCountForMissing); + + - //add zero allele counts for any reference alleles not seen in priors (if applicable) - final int existingRefCounts = totalAlleleCounts.getOrDefault(vc1.getReference(), 0); - totalAlleleCounts.put(vc1.getReference(), existingRefCounts + numRefSamplesFromMissingResources); + // now extract the counts of the alleles in vc1 + //if we allow deletion priors, then we need to harmonize the allele representations between vc1 and totalAlleleCounts + final Set allAllelesRemapped = totalAlleleCounts.keySet(); + final Set resourceOnlyAlleles = new HashSet<>(allAllelesRemapped); + resourceOnlyAlleles.removeAll(origAllelesRemapped); + + //this array will have the same allele ordering as the VC + double[] alleleCounts = new double[origAllelesRemapped.size()]; + for (int i=0; i globalFrequencyPriorDirichlet + totalAlleleCounts.getOrDefault(a, 0)).toArray(); + //put resource alleles not in input VC into non-ref, if applicable + int nonRefInd = vc1.getAlleleIndex(Allele.NON_REF_ALLELE); + if (nonRefInd != -1) { + //the non-ref "allele" gets a single pseudo count since in some ways it's one allele -- if we treated it as all alleles not present it would get infinite pseudocounts + alleleCounts[nonRefInd] = Math.max(opts.snpPriorDirichlet, opts.indelPriorDirichlet) + resourceOnlyAlleles.stream().mapToDouble(a -> totalAlleleCounts.get(a)).sum(); + } - final List likelihoods = vc1.getGenotypes().stream().map(g -> parseLikelihoods(g)).collect(Collectors.toList()); + final List likelihoods = vc1.getGenotypes().stream().map(g -> parsePosteriorsIntoProbSpace(g)).collect(Collectors.toList()); - //TODO: for now just use priors that are SNPs because indel priors will bias SNP calls - final boolean useFlatPriors = !vc1.isSNP() || (resources.isEmpty() && !useDiscoveredAC) || resources.stream().anyMatch(r -> !r.isSNP()) ; + final boolean useFlatPriors = (!vc1.isSNP() && opts.useFlatPriorsForIndels) || (resources.isEmpty() && !useDiscoveredACForMissing && numRefSamplesFromMissingResources == 0); - final List posteriors = calculatePosteriorProbs(likelihoods,alleleCounts,vc1.getMaxPloidy(2), useFlatPriors); + final List posteriors = calculatePosteriorProbs(likelihoods,alleleCounts,vc1.getMaxPloidy(HomoSapiensConstants.DEFAULT_PLOIDY), useFlatPriors); final GenotypesContext newContext = GenotypesContext.create(); for ( int genoIdx = 0; genoIdx < vc1.getNSamples(); genoIdx ++ ) { final GenotypeBuilder builder = new GenotypeBuilder(vc1.getGenotype(genoIdx)); builder.phased(vc1.getGenotype(genoIdx).isPhased()); if ( posteriors.get(genoIdx) != null ) { - GATKVariantContextUtils.makeGenotypeCall(vc1.getMaxPloidy(2), builder, + GATKVariantContextUtils.makeGenotypeCall(vc1.getMaxPloidy(HomoSapiensConstants.DEFAULT_PLOIDY), builder, GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, posteriors.get(genoIdx), vc1.getAlleles()); builder.attribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY, Utils.listFromPrimitives(GenotypeLikelihoods.fromLog10Likelihoods(posteriors.get(genoIdx)).getAsPLs())); @@ -71,15 +142,35 @@ public static VariantContext calculatePosteriorProbs(final VariantContext vc1, } final List priors = Utils.listFromPrimitives( - GenotypeLikelihoods.fromLog10Likelihoods(getDirichletPrior(alleleCounts, vc1.getMaxPloidy(2),useFlatPriors)).getAsPLs()); - - final VariantContextBuilder builder = new VariantContextBuilder(vc1).genotypes(newContext).attribute(GATKVCFConstants.GENOTYPE_PRIOR_KEY, priors); - // add in the AC, AF, and AN attributes - VariantContextUtils.calculateChromosomeCounts(builder, true); + GenotypeLikelihoods.fromLog10Likelihoods(getDirichletPrior(alleleCounts, vc1.getMaxPloidy(HomoSapiensConstants.DEFAULT_PLOIDY),useFlatPriors)).getAsPLs()); + + final VariantContextBuilder builder = new VariantContextBuilder(vc1).genotypes(newContext); + final boolean isHomRefBlock = vc1.getAlternateAlleles().size() == 1 && vc1.getAlleles().contains(Allele.NON_REF_ALLELE); + if (!isHomRefBlock) { + // update/add in the AC, AF, and AN attributes and genotype prior -- this is kind of a cheat because we're doing it + // outside the annotation engine, which has the header line responsibility for these fields. For CGP the + // headers should already be there, but for HaplotypeCaller GVCF mode we'll add the headers in HaplotypeCallerEngine::makeVCFHeader. + VariantContextUtils.calculateChromosomeCounts(builder.attribute(GATKVCFConstants.GENOTYPE_PRIOR_KEY, priors), true); + } return builder.make(); } - private static double[] parseLikelihoods(Genotype genotype) { + public static int[] parsePosteriorsIntoPhredSpace(Genotype genotype) { + final Object PPfromVCF = genotype.getExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY); + + if (PPfromVCF == null){ + return genotype.getPL(); + } else if (PPfromVCF instanceof String) { + final String PPstring = (String) PPfromVCF; + //samples not in trios will have PP tag like ".,.,." if family priors are applied + return PPstring.charAt(0)=='.' ? genotype.getPL() : + Arrays.stream(PPstring.split(",")).mapToInt(i -> Integer.parseInt(i)).toArray(); + } else { + return Arrays.stream(extractInts(PPfromVCF)).toArray(); + } + } + + public static double[] parsePosteriorsIntoProbSpace(Genotype genotype) { final Object PPfromVCF = genotype.getExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY); if (PPfromVCF == null){ @@ -196,7 +287,7 @@ static double[] getDirichletPrior(final double[] knownCountsByAllele, final int * @param context - line to be parsed from the input VCF file * @param useAC - use allele count annotation value from VariantContext (vs. MLEAC) */ - private static void addAlleleCounts(final Map counts, final VariantContext context, final boolean useAC) { + private static void addAlleleCounts(final Map counts, final VariantContext context, final List remappedAlleles, final boolean useAC) { final int[] ac; //use MLEAC value... if ( context.hasAttribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY) && ! useAC ) { @@ -215,18 +306,20 @@ else if ( context.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { } } - //since the allele count for the reference allele is not given in the VCF format, - //calculate it from the allele number minus the total counts for alternate alleles - for ( final Allele allele : context.getAlleles() ) { + for ( int i = 0; i < context.getAlleles().size(); i++ ) { + final Allele allele = remappedAlleles.get(i); + final Allele origAllele = context.getAlleles().get(i); final int count; if ( allele.isReference() ) { + //since the allele count for the reference allele is not given in the VCF format, + //calculate it from the allele number minus the total counts for alternate alleles if ( context.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) { count = Math.max(context.getAttributeAsInt(VCFConstants.ALLELE_NUMBER_KEY,-1) - (int) MathUtils.sum(ac),0); //occasionally an MLEAC value will sneak in that's greater than the AN } else { count = Math.max(context.getCalledChrCount() - (int) MathUtils.sum(ac),0); } } else { - count = ac[context.getAlternateAlleles().indexOf(allele)]; + count = ac[context.getAlternateAlleles().indexOf(origAllele)]; } //if this allele isn't in the map yet, add it if ( ! counts.containsKey(allele) ) { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java index a42a8a369d6..2234f3a39ca 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java @@ -1,6 +1,7 @@ package org.broadinstitute.hellbender.utils; import org.apache.commons.math3.distribution.EnumeratedDistribution; +import org.apache.commons.math3.exception.DimensionMismatchException; import org.apache.commons.math3.exception.NotStrictlyPositiveException; import org.apache.commons.math3.exception.NumberIsTooLargeException; import org.apache.commons.math3.linear.RealMatrix; @@ -358,6 +359,27 @@ public static double[] posteriors(double[] log10Priors, double[] log10Likelihood return normalizeFromLog10ToLinearSpace(MathArrays.ebeAdd(log10Priors, log10Likelihoods)); } + public static int[] normalizePLs(int[] PLs) { + final int[] newPLs = new int[PLs.length]; + final int smallest = arrayMin(PLs); + for(int i=0; i double[] function mapped to an index range public static double[] sumArrayFunction(final int min, final int max, final IntToDoubleArrayFunction function) { Utils.validateArg(max >= min, "max must be at least as great as min"); @@ -1187,6 +1209,17 @@ public static double arrayMax(final double[] array) { return array[maxElementIndex(array)]; } + public static int arrayMin(final int[] array) { + Utils.nonNull(array); + int min=array[0]; + for(int i=0; i allAlleles) { + public static AlleleMapper resolveIncompatibleAlleles(final Allele refAllele, final VariantContext vc, final LinkedHashSet allAlleles) { if ( refAllele.equals(vc.getReference()) ) return new AlleleMapper(vc); else { @@ -914,7 +914,7 @@ private static AlleleMapper resolveIncompatibleAlleles(final Allele refAllele, f * @param currentAlleles the list of alleles already created * @return a non-null mapping of original alleles to new (extended) ones */ - private static Map createAlleleMapping(final Allele refAllele, + public static Map createAlleleMapping(final Allele refAllele, final VariantContext oneVC, final Collection currentAlleles) { final Allele myRef = oneVC.getReference(); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/writers/HomRefBlock.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/writers/HomRefBlock.java index fa744e1ecc2..d789b5c7b69 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/variant/writers/HomRefBlock.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/writers/HomRefBlock.java @@ -8,6 +8,7 @@ import htsjdk.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.hellbender.exceptions.GATKException; +import org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils; import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; @@ -38,6 +39,7 @@ final class HomRefBlock implements Locatable { private int end; private int[] minPLs = null; + private int[] minPPs = null; /** * Create a new HomRefBlock @@ -83,10 +85,14 @@ private Genotype createHomRefGenotype(String sampleName) { gb.noAD().noPL().noAttributes(); // clear all attributes final int[] minPLs = getMinPLs(); + final int[] minPPs = getMinPPs(); gb.PL(minPLs); - gb.GQ(GATKVariantContextUtils.calculateGQFromPLs(minPLs)); + gb.GQ(GATKVariantContextUtils.calculateGQFromPLs(minPPs != null? minPPs : minPLs)); gb.DP(getMedianDP()); gb.attribute(GATKVCFConstants.MIN_DP_FORMAT_KEY, getMinDP()); + if (minPPs != null) { + gb.attribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY, Utils.listFromPrimitives(minPPs)); + } return gb.make(); } @@ -112,7 +118,8 @@ public void add(final int pos, final Genotype genotype) { if( minPLs == null ) { minPLs = genotype.getPL(); - } else { // otherwise take the min with the provided genotype's PLs + } + else { // otherwise take the min with the provided genotype's PLs final int[] pls = genotype.getPL(); if (pls.length != minPLs.length) { throw new GATKException("trying to merge different PL array sizes: " + pls.length + " != " + minPLs.length); @@ -121,6 +128,22 @@ public void add(final int pos, final Genotype genotype) { minPLs[i] = Math.min(minPLs[i], pls[i]); } } + + if( genotype.hasExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)) { + if (minPPs == null ) { + minPPs = PosteriorProbabilitiesUtils.parsePosteriorsIntoPhredSpace(genotype); + } + else { // otherwise take the min with the provided genotype's PLs + final int[] pps = PosteriorProbabilitiesUtils.parsePosteriorsIntoPhredSpace(genotype); + if (pps.length != minPPs.length) { + throw new GATKException("trying to merge different PP array sizes: " + pps.length + " != " + minPPs.length); + } + for (int i = 0; i < pps.length; i++) { + minPPs[i] = Math.min(minPPs[i], pps[i]); + } + } + } + end = pos; DPs.add(Math.max(genotype.getDP(), 0)); // DP must be >= 0 } @@ -150,6 +173,11 @@ public int[] getMinPLs() { return minPLs; } + /** Get the min PPs observed within this band, can be null if no PPs have yet been observed */ + public int[] getMinPPs() { + return minPPs; + } + int getGQUpperBound() { return maxGQ; } 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 60e65808a00..e5b67a979c2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java @@ -100,6 +100,14 @@ public Object[][] gvcfsToGenotype() { }; } + @DataProvider(name = "gvcfWithPPs") + public Object[][] gvcfWithPPs() { + return new Object[][] { + {getTestFile("../../haplotypecaller/expected.testGVCFMode.gatk4.posteriors.g.vcf"), + getTestFile( "expected.posteriors.genotyped.vcf"), NO_EXTRA_ARGS, b37_reference_20_21} + }; + } + /* This test is useful for testing changes in GATK4 versus different versions of GATK3. @@ -180,17 +188,24 @@ public void testEntireVariantContext(File input, File expected, List ext private void assertVariantContextsMatch(File input, File expected, List extraArgs, String reference) throws IOException { try { - final VCFHeader header = VCFHeaderReader.readHeaderFrom(new SeekablePathStream( IOUtils.getPath(expected.getAbsolutePath()))); - runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE ,header), reference); + final VCFHeader header = VCFHeaderReader.readHeaderFrom(new SeekablePathStream(IOUtils.getPath(expected.getAbsolutePath()))); + runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, ATTRIBUTES_TO_IGNORE, header), reference); } catch (java.io.IOException e) { throw new AssertionError("There was a problem reading your expected input file"); } } + private void assertGenotypesMatch(File input, File expected, List additionalArguments, String reference) throws IOException { runGenotypeGVCFSAndAssertSomething(input, expected, additionalArguments, VariantContextTestUtils::assertVariantContextsHaveSameGenotypes, reference); } + @Test(dataProvider = "gvcfWithPPs") + public void assertPPsAreStripped(File input, File expected, List extraArgs, String reference) throws IOException { + runGenotypeGVCFSAndAssertSomething(input, expected, extraArgs, VariantContextTestUtils::assertGenotypePosteriorsAttributeWasRemoved, reference); + } + + private void runGenotypeGVCFSAndAssertSomething(File input, File expected, List additionalArguments, BiConsumer assertion, String reference) throws IOException { runGenotypeGVCFSAndAssertSomething(input.getAbsolutePath(), expected, additionalArguments, assertion, reference ); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 0b21b903912..690df5ff5e7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -5,6 +5,7 @@ import htsjdk.tribble.Tribble; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeader; @@ -18,6 +19,9 @@ import org.broadinstitute.hellbender.engine.ReadsDataSource; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils; +import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection; +import org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors; +import org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils; import org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection; import org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2IntegrationTest; import org.broadinstitute.hellbender.utils.SimpleInterval; @@ -28,6 +32,7 @@ import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import org.testng.Assert; import org.testng.annotations.DataProvider; @@ -296,6 +301,44 @@ public void testGVCFModeIsConcordantWithGATK3_8AlelleSpecificResults(final Strin Assert.assertTrue(concordance >= 0.99, "Concordance with GATK 3.8 in AS GVCF mode is < 99% (" + concordance + ")"); } + @Test + public void testGVCFModeGenotypePosteriors() throws Exception { + Utils.resetRandomGenerator(); + + final String inputFileName = NA12878_20_21_WGS_bam; + final String referenceFileName =b37_reference_20_21; + + final File output = createTempFile("testGVCFModeIsConsistentWithPastResults", ".g.vcf"); + + final String[] args = { + "-I", inputFileName, + "-R", referenceFileName, + "-L", "20:10000000-10100000", + "-O", output.getAbsolutePath(), + "-ERC", "GVCF", + "--" + GenotypeCalculationArgumentCollection.SUPPORTING_CALLSET_LONG_NAME, + largeFileTestDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf", + "--" + GenotypeCalculationArgumentCollection.NUM_REF_SAMPLES_LONG_NAME, "2500", + "-pairHMM", "AVX_LOGLESS_CACHING", + "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false" + }; + + runCommandLine(args); + + Pair> results = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath()); + + for (final VariantContext vc : results.getRight()) { + final Genotype g = vc.getGenotype(0); + Assert.assertTrue(g.hasExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + if (isGVCFReferenceBlock(vc) ) { + Assert.assertTrue(!vc.hasAttribute(GATKVCFConstants.GENOTYPE_PRIOR_KEY)); + } + else if (!vc.getAlternateAllele(0).equals(Allele.NON_REF_ALLELE)){ //there are some variants that don't have non-symbolic alts + Assert.assertTrue(vc.hasAttribute(GATKVCFConstants.GENOTYPE_PRIOR_KEY)); + } + } + } + @Test public void testGenotypeGivenAllelesMode() throws IOException { Utils.resetRandomGenerator(); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index 1d3ed6803a8..eb762408c2b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -55,7 +55,7 @@ public void setUp() { @BeforeMethod public void setupModel() { - model = new ReferenceConfidenceModel(samples, header, 10); + model = new ReferenceConfidenceModel(samples, header, 10, -1); } @DataProvider(name = "CalcNIndelInformativeReadsData") @@ -257,7 +257,7 @@ public void testRefConfidenceBasic(final int nReads, final int extension) { final PloidyModel ploidyModel = new HomogeneousPloidyModel(samples,2); final IndependentSampleGenotypesModel genotypingModel = new IndependentSampleGenotypesModel(); final List expectedDPs = Collections.nCopies(data.getActiveRegion().getSpan().size(), nReads); - final List contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls); + final List contexts = model.calculateRefConfidence(data.getRefHap(), haplotypes, data.getPaddedRefLoc(), data.getActiveRegion(), likelihoods, ploidyModel, calls, false, Collections.emptyList()); checkReferenceModelResult(data, contexts, expectedDPs, calls); } diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index b8c6a03620b..069df4a128f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -26,6 +26,35 @@ public final class CalculateGenotypePosteriorsIntegrationTest extends CommandLin private String CEUtrioMixedPloidyTest = dir + "CEUtrioMixedPloidy.vcf"; private String getThreeMemberNonTrioTest = dir + "threeMemberNonTrioTest_chr1.vcf"; + @Test + public void testDefaultsWithPanel() throws IOException { + final IntegrationTestSpec spec = new IntegrationTestSpec( + " -O %s" + + " -R " + b37_reference_20_21 + //NOTE: we need a reference for -L + " -L 20:10,000,000-10,010,000" + + " -" +CalculateGenotypePosteriors.SUPPORTING_CALLSETS_SHORT_NAME + " " + largeDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf" + + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false" + + " -V " + dir + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf", + Collections.singletonList(dir + "expectedCGP_testDefaultsWithPanel.vcf") + ); + spec.executeTest("testDefaultsWithPanel", this); + } + + @Test + public void testNumRefWithPanel() throws IOException { + final IntegrationTestSpec spec = new IntegrationTestSpec( + " -O %s" + + " -R " + b37_reference_20_21 + //NOTE: we need a reference for -L + " -L 20:10,000,000-10,010,000" + + " -" +CalculateGenotypePosteriors.SUPPORTING_CALLSETS_SHORT_NAME + " " + largeDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf" + + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false" + + " -V " + dir + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" + + " --" + CalculateGenotypePosteriors.NUM_REF_SAMPLES_LONG_NAME + " 2500", + Collections.singletonList(dir + "expectedCGP_testNumRefWithPanel.vcf") + ); + spec.executeTest("testDefaultsWithPanel", this); + } + @Test //use the first 20 variants to save time; they have a nice range of AC from 4 to over 4000 public void testUsingDiscoveredAF() throws IOException { diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtilsUnitTest.java index c96ce8e01de..5c43604b682 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtilsUnitTest.java @@ -6,23 +6,34 @@ import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; +import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import org.testng.Assert; import org.testng.annotations.Test; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; +import java.util.*; @SuppressWarnings("unchecked") public final class PosteriorProbabilitiesUtilsUnitTest extends GATKBaseTest { final Allele Aref = Allele.create("A", true); + final Allele ATCref = Allele.create("ATC", true); + final Allele ATCTCref = Allele.create("ATCTC", true); + final Allele TTCTC = Allele.create("TTCTC", false); + final Allele Aalt = Allele.create("A", false); final Allele T = Allele.create("T"); final Allele C = Allele.create("C"); final Allele ATC = Allele.create("ATC"); final Allele ATCATC = Allele.create("ATCATC"); + final boolean useInputSamplesAlleleCounts = true; + final boolean useMLEAC = true; + final boolean useFlatPriorsForMissingResources = false; + final boolean useFlatPriorsForIndels = false; + + private PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions defaultOptions = + new PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions(0.001, 0.0001, useInputSamplesAlleleCounts, useMLEAC, useFlatPriorsForMissingResources, useFlatPriorsForIndels); + private String arraysEq(final int[] a, final int[] b) { if ( a.length != b.length ) { return String.format("NEQ: %s | %s", Arrays.toString(a), Arrays.toString(b)); @@ -45,9 +56,17 @@ private int[] _mleparse(final List s) { return mle; } - private Genotype makeGwithPLs(final String sample, final Allele a1, final Allele a2, final double[] pls) { - final Genotype gt = new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make(); - if ( pls != null && pls.length > 0 ) { + /** + * Create a genotype for sample with genotype a1/a2 and PLs derived from log10GLs + * @param sample sample name + * @param a1 sample genotype allele 1 + * @param a2 sample genotype allele 2 + * @param log10GLs log10-scaled genotype likelihoods (NOT Phred-scaled) + * @return a Genotype + */ + private Genotype makeGwithLog10GLs(final String sample, final Allele a1, final Allele a2, final double[] log10GLs) { + final Genotype gt = new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(log10GLs).make(); + if ( log10GLs != null && log10GLs.length > 0 ) { Assert.assertNotNull(gt.getPL()); Assert.assertTrue(gt.getPL().length > 0); for ( final int i : gt.getPL() ) { @@ -66,17 +85,41 @@ private Genotype makeG(final String sample, final Allele a1, final Allele a2, fi return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make(); } + //NOTE: for deletions use the method makeDeletionVC so stop position validates private VariantContext makeVC(final String source, final List alleles, final Genotype... genotypes) { final int start = 10; - final int stop = start; // alleles.contains(ATC) ? start + 3 : start; + final int stop = start; + return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).make(); + } + + private VariantContext makeDeletionVC(final String source, final List alleles, final int refLength, final Genotype... genotypes) { + final int start = 10; + final int stop = start+refLength-1; return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).make(); } + private VariantContext makeHomRefBlock(final String source, final Allele refAllele, final Genotype... genotypes) { + final int start = 10; + final int stop = start; + final Map infoMap = new HashMap<>(); + infoMap.put(VCFConstants.END_KEY,100); + final List alleles = new ArrayList<>(); + alleles.add(refAllele); + alleles.add(Allele.NON_REF_ALLELE); + return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).attributes(infoMap).make(); + } + @Test public void testCalculatePosteriorNoExternalData() { - VariantContext test1 = makeVC("1", Arrays.asList(Aref,T), makeG("s1",Aref,T,20,0,10), - makeG("s2",T,T,60,40,0), - makeG("s3",Aref,Aref,0,30,90), + final int numSamples = 12; + final int AN = HomoSapiensConstants.DEFAULT_PLOIDY*numSamples; + final int MLEAC = 12; + final int[] sample0PLs = {20,0,10}; + final int[] sample1PLs = {60,40,0}; + final int[] sample2PLs = {0,30,90}; + VariantContext test1 = makeVC("1", Arrays.asList(Aref,T), makeG("s1",Aref,T,sample0PLs), + makeG("s2",T,T,sample1PLs), + makeG("s3",Aref,Aref,sample2PLs), makeG("s4",Aref,T,20,0,10), makeG("s5",T,T,60,40,0), makeG("s6",Aref,Aref,0,30,90), @@ -86,24 +129,33 @@ public void testCalculatePosteriorNoExternalData() { makeG("s10",Aref,T,20,0,10), makeG("s11",T,T,60,40,0), makeG("s12",Aref,Aref,0,30,90)); - test1 = new VariantContextBuilder(test1).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,12).make(); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(test1, new ArrayList<>(), 0, 0.001, true, false, false); - final Genotype test1exp1 = makeGwithPLs("s1",Aref,T,new double[]{-2.26110257, -0.02700903, -1.26110257}); - Assert.assertTrue(test1exp1.hasPL()); - final Genotype test1exp2 = makeGwithPLs("s2",T,T,new double[]{-6.000075e+00, -3.765981e+00, -7.488009e-05}); - final Genotype test1exp3 = makeGwithPLs("s3",Aref,Aref,new double[]{-0.0007438855, -2.7666503408, -9.0007438855}); + test1 = new VariantContextBuilder(test1).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,MLEAC).make(); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(test1, new ArrayList<>(), 0, defaultOptions); + final double[] alleleCounts = {AN-MLEAC, MLEAC}; + //prior = {3,0,3} + final int[] prior = GenotypeLikelihoods.fromLog10Likelihoods(PosteriorProbabilitiesUtils.getDirichletPrior(alleleCounts, test1.getMaxPloidy(HomoSapiensConstants.DEFAULT_PLOIDY),false)).getAsPLs(); + final int[] sample0expected = MathUtils.normalizePLs(MathUtils.ebeAdd(sample0PLs, prior)); + final int[] sample1expected = MathUtils.normalizePLs(MathUtils.ebeAdd(sample1PLs, prior)); + final int[] sample2expected = MathUtils.normalizePLs(MathUtils.ebeAdd(sample2PLs, prior)); + Assert.assertTrue(List.class.isAssignableFrom(test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY).getClass())); - Assert.assertEquals(arraysEq(test1exp1.getPL(), _mleparse((List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); - Assert.assertEquals(arraysEq(test1exp2.getPL(),_mleparse((List)test1result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); - Assert.assertEquals(arraysEq(test1exp3.getPL(),_mleparse((List)test1result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + Assert.assertEquals(arraysEq(sample0expected, _mleparse((List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + Assert.assertEquals(arraysEq(sample1expected,_mleparse((List)test1result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + Assert.assertEquals(arraysEq(sample2expected,_mleparse((List)test1result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); // AA AB BB AC BC CC // AA AC CC AT CT TT + final int nSamplesTest2 = 12; + final int ANTest2 = HomoSapiensConstants.DEFAULT_PLOIDY*nSamplesTest2; + final int[] sample0PLsTest2 = {30,10,60,0,15,90}; + final int[] sample1PLsTest2 = {40,0,10,30,40,80}; + final int[] sample2PLsTest2 = {0,5,8,15,20,40}; + final int[] sample3PLsTest2 = {80,40,12,20,0,10}; VariantContext test2 = makeVC("2", Arrays.asList(Aref,C,T), - makeG("s1",Aref,T,30,10,60,0,15,90), - makeG("s2",Aref,C,40,0,10,30,40,80), - makeG("s3",Aref,Aref,0,5,8,15,20,40), - makeG("s4",C,T,80,40,12,20,0,10), + makeG("s1",Aref,T,sample0PLsTest2), + makeG("s2",Aref,C,sample1PLsTest2), + makeG("s3",Aref,Aref,sample2PLsTest2), + makeG("s4",C,T,sample3PLsTest2), makeG("s5",Aref,T,30,10,60,0,15,90), makeG("s6",Aref,C,40,0,10,30,40,80), makeG("s7",Aref,Aref,0,5,8,15,20,40), @@ -112,16 +164,22 @@ public void testCalculatePosteriorNoExternalData() { makeG("s10",Aref,C,40,0,10,30,40,80), makeG("s11",Aref,Aref,0,5,8,15,20,40), makeG("s12",C,T,80,40,12,20,0,10)); - test2 = new VariantContextBuilder(test2).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, new ArrayList<>(Arrays.asList(6, 6))).make(); - final VariantContext test2result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(test2, new ArrayList<>(),5,0.001,true,false, false); - final Genotype test2exp1 = makeGwithPLs("s1",Aref,T,new double[]{-2.823957, -1.000000, -6.686344, 0.000000, -1.952251, -9.686344}); - final Genotype test2exp2 = makeGwithPLs("s2",Aref,C,new double[]{-3.823957, 0.000000, -1.686344, -3.000000, -4.452251, -8.686344}); - final Genotype test2exp3 = makeGwithPLs("s3",Aref,Aref,new double[] {0.000000, -0.676043, -1.662387, -1.676043, -2.628294, -4.862387}); - final Genotype test2exp4 = makeGwithPLs("s4",C,T,new double[]{-7.371706, -3.547749, -1.434094, -1.547749, 0.000000, -1.234094}); - Assert.assertEquals(arraysEq(test2exp1.getPL(), _mleparse((List)test2result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); - Assert.assertEquals(arraysEq(test2exp2.getPL(), _mleparse((List)test2result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); - Assert.assertEquals(arraysEq(test2exp3.getPL(), _mleparse((List)test2result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); - Assert.assertEquals(arraysEq(test2exp4.getPL(), _mleparse((List)test2result.getGenotype(3).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + + final int MLEAC1 = 6; + final int MLEAC2 = 6; + test2 = new VariantContextBuilder(test2).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, new ArrayList<>(Arrays.asList(MLEAC1, MLEAC2))).make(); + final double[] alleleCountsTest2 = {ANTest2-MLEAC1-MLEAC2, MLEAC1, MLEAC2}; + //multiPrior = {0,0,6,0,3,6}; + final int[] multiPrior = GenotypeLikelihoods.fromLog10Likelihoods(PosteriorProbabilitiesUtils.getDirichletPrior(alleleCountsTest2, test1.getMaxPloidy(HomoSapiensConstants.DEFAULT_PLOIDY),false)).getAsPLs(); + final VariantContext test2result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(test2, new ArrayList<>(), 0, defaultOptions); + final int[] sample0expectedTest2 = MathUtils.normalizePLs(MathUtils.ebeAdd(sample0PLsTest2, multiPrior)); + final int[] sample1expectedTest2 = MathUtils.normalizePLs(MathUtils.ebeAdd(sample1PLsTest2, multiPrior)); + final int[] sample2expectedTest2 = MathUtils.normalizePLs(MathUtils.ebeAdd(sample2PLsTest2, multiPrior)); + final int[] sample3expectedTest2 = MathUtils.normalizePLs(MathUtils.ebeAdd(sample3PLsTest2, multiPrior)); + Assert.assertEquals(arraysEq(sample0expectedTest2, _mleparse((List)test2result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + Assert.assertEquals(arraysEq(sample1expectedTest2, _mleparse((List)test2result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + Assert.assertEquals(arraysEq(sample2expectedTest2, _mleparse((List)test2result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); + Assert.assertEquals(arraysEq(sample3expectedTest2, _mleparse((List)test2result.getGenotype(3).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); } @Test @@ -135,19 +193,19 @@ public void testCalculatePosteriorSamplePlusExternal() { supplTest1.add(makeVC("4", Arrays.asList(Aref,T), makeG("s_1",T,T), makeG("s_2",Aref,T))); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false, false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1, 0, defaultOptions); // the counts here are ref=30, alt=14 - final Genotype test1exp1 = makeGwithPLs("t1",T,T,new double[]{-3.370985, -1.415172, -0.01721766}); - final Genotype test1exp2 = makeGwithPLs("t2",Aref,T,new double[]{-1.763792, -0.007978791, -3.010024}); - final Genotype test1exp3 = makeGwithPLs("t3",Aref,T,new double[]{-2.165587, -0.009773643, -1.811819}); + final Genotype test1exp1 = makeGwithLog10GLs("t1",T,T,new double[]{-3.370985, -1.415172, -0.01721766}); + final Genotype test1exp2 = makeGwithLog10GLs("t2",Aref,T,new double[]{-1.763792, -0.007978791, -3.010024}); + final Genotype test1exp3 = makeGwithLog10GLs("t3",Aref,T,new double[]{-2.165587, -0.009773643, -1.811819}); Assert.assertEquals(arraysEq(test1exp1.getPL(),_mleparse((List) test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); Assert.assertEquals(arraysEq(test1exp2.getPL(),_mleparse((List) test1result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); Assert.assertEquals(arraysEq(test1exp3.getPL(),_mleparse((List) test1result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); final VariantContext testNonOverlapping = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,3,1,0)); final List other = Arrays.asList(makeVC("2", Arrays.asList(Aref,C),makeG("s2",C,C,10,2,0))); - final VariantContext test2result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testNonOverlapping,other,0,0.001,true,false,false); - final Genotype test2exp1 = makeGwithPLs("SGV",T,T,new double[]{-4.078345, -3.276502, -0.0002661066}); + final VariantContext test2result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testNonOverlapping,other,0, defaultOptions); + final Genotype test2exp1 = makeGwithLog10GLs("SGV",T,T,new double[]{-4.078345, -3.276502, -0.0002661066}); Assert.assertEquals(arraysEq(test2exp1.getPL(),_mleparse((List) test2result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); } @@ -156,7 +214,7 @@ public void testCalculatePosteriorHOM_VARtoHET() { final VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,1,0)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,500).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); final int[] GP = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); Assert.assertTrue(GP[2] > GP[1]); @@ -167,7 +225,7 @@ public void testCalculatePosteriorHETtoHOM_VAR() { final VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,0,1)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,900).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); final int[] GP = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); Assert.assertTrue(GP[2] < GP[1]); @@ -178,7 +236,7 @@ public void testCalculatePosteriorHOM_REFtoHET() { final VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,0,1,40)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,500).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); final int[] GP = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); Assert.assertTrue(GP[0] > GP[1]); @@ -189,7 +247,7 @@ public void testCalculatePosteriorHETtoHOM_REF() { final VariantContext testOverlappingBase = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,1,0,40)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,100).attribute(VCFConstants.ALLELE_NUMBER_KEY,1000).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); final int[] GP = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); Assert.assertTrue(GP[0] < GP[1]); @@ -202,7 +260,7 @@ public void testMLEACgreaterThanAN() { makeG("s3",Aref,T,22,0,12)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,11).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); } @Test(expectedExceptions = {UserException.class}) @@ -213,7 +271,7 @@ public void testWrongNumberACvalues() { final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T,C))).attribute(VCFConstants.ALLELE_COUNT_KEY,5).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); } @Test(expectedExceptions = {UserException.class}) @@ -223,7 +281,7 @@ public void testWrongNumberMLEACvalues() { makeG("s3",Aref,T,22,0,12)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T,C))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY,5).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); } @Test @@ -233,7 +291,7 @@ public void testMultipleACvalues() { makeG("s3",Aref,T,22,0,12)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T,C))).attribute(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); } @Test @@ -243,35 +301,94 @@ public void testMultipleMLEACvalues() { makeG("s3",Aref,T,22,0,12)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T,C))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,0.001,true,false,false); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(testOverlappingBase,supplTest1,0,defaultOptions); } @Test public void testInputIndel() { final VariantContext inputIndel = makeVC("1", Arrays.asList(Aref, ATC), makeG("s1",ATC,ATC,40,20,0), makeG("s2",Aref,ATC,18,0,24), - makeG("s3",Aref,ATC,22,0,12)); + makeG("s3",Aref,ATC,22,0,12), + makeG("s5",Aref,Aref,0,15,90), + makeG("s6",Aref,ATC,40,0,10), + makeG("s7",Aref,Aref,0,5,8), + makeG("s8",Aref,ATC,20,0,10), + makeG("s9",Aref,Aref,0,15,90), + makeG("s10",Aref,ATC,40,0,10), + makeG("s11",Aref,Aref,0,5,8), + makeG("s12",ATC,ATC,20,0,10)); final List supplTest1 = new ArrayList<>(1); supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T,C))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(inputIndel,supplTest1,0,0.001,true,false,false); - - final int[] GPs = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); - final int[] PLs = test1result.getGenotype(0).getPL(); - Assert.assertEquals(PLs,GPs); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(inputIndel,supplTest1,0,defaultOptions); + + final int[] sample0_PPs = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final int[] sample0_expectedPPs = {36,16,0}; + Assert.assertEquals(sample0_PPs,sample0_expectedPPs); + final int[] sample1_PPs = _mleparse( (List)test1result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final int[] sample1_expectedPPs = {19,0,28}; + Assert.assertEquals(sample1_PPs,sample1_expectedPPs); + final int[] sample2_PPs = _mleparse( (List)test1result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final int[] sample2_expectedPPs = {23,0,16}; + Assert.assertEquals(sample2_PPs,sample2_expectedPPs); } @Test public void testPriorIndel() { - final VariantContext inputIndel = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0), + final VariantContext inputSNP = makeVC("1", Arrays.asList(Aref,T), makeG("s1",T,T,40,20,0), makeG("s2",Aref,T,18,0,24), makeG("s3",Aref,T,22,0,12)); - final List supplTest1 = new ArrayList<>(1); - supplTest1.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,ATC,ATCATC))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); - final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(inputIndel,supplTest1,0,0.001,true,false,false); + final List indelResource = new ArrayList<>(1); + indelResource.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,ATC,ATCATC))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, Arrays.asList(5,4)).attribute(VCFConstants.ALLELE_NUMBER_KEY,10).make()); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(inputSNP,indelResource,0,defaultOptions); + + final int[] sample0_PPs = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final int[] sample0_expectedPPs = {42,19,0}; + Assert.assertEquals(sample0_PPs,sample0_expectedPPs); + final int[] sample1_PPs = _mleparse( (List)test1result.getGenotype(1).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final int[] sample1_expectedPPs = {21,0,25}; + Assert.assertEquals(sample1_PPs,sample1_expectedPPs); + final int[] sample2_PPs = _mleparse( (List)test1result.getGenotype(2).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final int[] sample2_expectedPPs = {25,0,13}; + Assert.assertEquals(sample2_PPs,sample2_expectedPPs); + } - final int[] GPs = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); - final int[] PLs = test1result.getGenotype(0).getPL(); - Assert.assertEquals(PLs,GPs); + @Test + public void testRefConfHomRefAttributes() { + //20 10001432 . A . . END=10001432 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:40:56:0,18,270:0,40,320 + final VariantContext homRefBlock = makeVC("1", Arrays.asList(Aref,Allele.NON_REF_ALLELE), makeG("s1",Aref,Aref,0,18,270)); + final List resource = new ArrayList<>(1); + resource.add(new VariantContextBuilder(makeVC("2", Arrays.asList(Aref,T))).attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, 16).attribute(VCFConstants.ALLELE_NUMBER_KEY,5060).make()); + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(homRefBlock,resource,0,defaultOptions); + + //Keep PLs and add PPs + final Genotype g = test1result.getGenotype(0); + Assert.assertTrue(g.hasPL()); + Assert.assertTrue(g.hasExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + int[] PP = _mleparse( (List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + //GQ should be based on PPs, not on PLs + Assert.assertTrue(g.hasGQ()); + Assert.assertTrue(MathUtils.secondSmallestMinusSmallest(PP,0) == g.getGQ()); + + } + + @Test + public void testDifferentRefAllelesAndNonRefCounts() { + final int[] sample1PLs = {934,0,1248,1042,1332,2374}; + final int MLEAC1 = 43; + final int MLEAC2 = 4005; + final int MLEAC3 = 37; + final int AN = 5060; + final VariantContext inputDeletion = makeDeletionVC("1", Arrays.asList(ATCref,Aalt,Allele.NON_REF_ALLELE), 3, makeG("s1",ATCref,Aalt,sample1PLs)); + final List indelResource = new ArrayList<>(1); + indelResource.add(new VariantContextBuilder(makeDeletionVC("2", Arrays.asList(ATCTCref,ATC,Aalt,TTCTC),5)). + attribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, Arrays.asList(MLEAC1,MLEAC2,MLEAC3)).attribute(VCFConstants.ALLELE_NUMBER_KEY,AN).make()); + final double[] alleleCounts = {AN-MLEAC1-MLEAC2-MLEAC3+HomoSapiensConstants.SNP_HETEROZYGOSITY, MLEAC1+HomoSapiensConstants.INDEL_HETEROZYGOSITY, MLEAC2+MLEAC3+HomoSapiensConstants.SNP_HETEROZYGOSITY}; + + final VariantContext test1result = PosteriorProbabilitiesUtils.calculatePosteriorProbs(inputDeletion,indelResource,0,defaultOptions); + final int[] multiPrior = GenotypeLikelihoods.fromLog10Likelihoods(PosteriorProbabilitiesUtils.getDirichletPrior(alleleCounts, inputDeletion.getMaxPloidy(HomoSapiensConstants.DEFAULT_PLOIDY),false)).getAsPLs(); + final int[] expectedPPs = MathUtils.normalizePLs(MathUtils.ebeAdd(sample1PLs, multiPrior)); + + Assert.assertEquals(arraysEq(expectedPPs, _mleparse((List)test1result.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY))), ""); } private double[] pl2gl(final int[] pl) { diff --git a/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java index 6a51f68634e..f3c2fdcc08f 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java @@ -11,6 +11,7 @@ import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.hellbender.engine.FeatureDataSource; +import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.GATKBaseTest; @@ -142,6 +143,16 @@ private static VariantContext makeVariantContext(VariantContextBuilder vcb, List return vcb.genotypes(gb.make()).id(VCFConstants.EMPTY_ID_FIELD).make(); } + private static VariantContext makeVariantContext(VariantContextBuilder vcb, List alleles, int gq, int[] PPs) { + final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, alleles); + gb.DP(10); + gb.AD(new int[]{1, 2}); + gb.PL(new int[]{0, gq, 20+gq}); + gb.attribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY, Utils.listFromPrimitives(PPs)); + gb.GQ(MathUtils.secondSmallestMinusSmallest(PPs, gq)); + return vcb.genotypes(gb.make()).id(VCFConstants.EMPTY_ID_FIELD).make(); + } + @Test public void testCloseEmitsLastVariant() { final MockWriter mockWriter = new MockWriter(); @@ -245,6 +256,19 @@ public void testCrossingContigBoundaryNonRefThenNonRef() { assertGoodVC(mockWriter.emitted.get(1), CHR2, 1, 1, true); } + @SuppressWarnings("unchecked") + private static void assertGoodVCwithPPs(final VariantContext vc, final String contig, final int start, final int stop, final boolean nonRef) { + final Genotype g = vc.getGenotype(SAMPLE_NAME); + Assert.assertTrue(g.hasExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY)); + final List PPs = (List)vc.getGenotype(0).getAnyAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY); + if (!nonRef) { + Assert.assertTrue(PPs.size() == 3); + Assert.assertTrue(g.hasGQ()); + Assert.assertTrue(PPs.get(1) == g.getGQ()); + } + assertGoodVC(vc, contig, start, stop, nonRef); + } + private static void assertGoodVC(final VariantContext vc, final String contig, final int start, final int stop, final boolean nonRef) { Assert.assertEquals(vc.getContig(), contig); Assert.assertEquals(vc.getStart(), start); @@ -303,7 +327,19 @@ public void testEmittingTwoBands() { } + @Test + public void testBandingUsingPP() { + final MockWriter mockWriter = new MockWriter(); + final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition, HomoSapiensConstants.DEFAULT_PLOIDY); + int[] PPs1 = {0,63,128}; + int[] PPs2 = {0,67,145}; + writer.add(makeVariantContext(new VariantContextBuilder("test", CHR1, 10000, 10000, ALLELES), Arrays.asList(REF, REF), 2, PPs1)); + writer.add(makeVariantContext(new VariantContextBuilder("test", CHR1, 10001, 10001, ALLELES), Arrays.asList(REF, REF), 21, PPs2)); + writer.close(); + Assert.assertEquals(mockWriter.emitted.size(), 1); + assertGoodVCwithPPs(mockWriter.emitted.get(0), CHR1, 10000, 10001, false); + } @Test diff --git a/src/test/resources/large/CalculateGenotypePosteriors/expectedCGP_testUsingDiscoveredAF.vcf b/src/test/resources/large/CalculateGenotypePosteriors/expectedCGP_testUsingDiscoveredAF.vcf index 8cb791517fc..1c51e4dcea4 100644 --- a/src/test/resources/large/CalculateGenotypePosteriors/expectedCGP_testUsingDiscoveredAF.vcf +++ b/src/test/resources/large/CalculateGenotypePosteriors/expectedCGP_testUsingDiscoveredAF.vcf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c1f2c47ae749b250447b608239cd3dde07921f218b6db2b6c5d34a936b41ab82 -size 1561420 +oid sha256:33a0ae12e592620bfa5352bc5e8fa4377fc820a37d50bff27e480c1b817de8df +size 1562713 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.posteriors.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.posteriors.g.vcf new file mode 100644 index 00000000000..c0b485289b6 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.posteriors.g.vcf @@ -0,0 +1,913 @@ +##fileformat=VCFv4.2 +##ALT= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) +##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) +##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) +##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) +##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) +##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) +##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) +##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) +##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) +##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) +##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) +##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) +##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) +##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) +##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) +##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) +##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) +##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) +##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) +##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) +##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) +##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) +##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) +##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) +##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) +##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) +##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) +##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) +##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) +##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) +##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) +##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) +##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) +##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) +##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) +##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) +##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) +##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) +##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) +##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) +##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) +##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) +##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) +##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) +##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) +##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) +##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) +##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) +##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) +##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) +##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) +##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) +##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) +##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) +##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) +##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) +##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) +##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) +##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) +##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) +##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) +##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) +##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) +##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) +##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10000000 . T . . END=10000116 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:99:64:0,120,1800:0,146,1857 +20 10000117 . C T, 905.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.136;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.913;PG=5,0,1,65,63,101;RAW_MQ=228169.00;ReadPosRankSum=-0.179 GT:AD:DP:GQ:PL:PP:SB 0/1:36,28,0:64:99:934,0,1248,1042,1332,2374:939,0,1249,1107,1395,2475:16,20,19,9 +20 10000118 . T . . END=10000210 GT:DP:GQ:MIN_DP:PL:PP 0/0:52:99:44:0,108,1620:0,172,1724 +20 10000211 . C T, 941.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.867;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.057;PG=5,0,1,65,63,101;RAW_MQ=192169.00;ReadPosRankSum=1.068 GT:AD:DP:GQ:PL:PP:SB 0/1:26,27,0:53:99:970,0,906,1049,988,2036:975,0,907,1114,1051,2137:15,11,11,16 +20 10000212 . A . . END=10000438 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:55:0,120,1800:0,142,1849 +20 10000439 . T G, 2804.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=279076.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,80,0:80:99:2833,240,0,2833,240,2833:2846,243,0,2902,303,2935:0,0,49,31 +20 10000440 . T . . END=10000597 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:99:41:0,93,1503:0,122,1566 +20 10000598 . T A, 1941.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=49;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=149628.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,49,0:49:99:1970,147,0,1970,147,1970:1983,150,0,2039,210,2072:0,0,19,30 +20 10000599 . T . . END=10000693 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:48:0,120,1800:0,184,1904 +20 10000694 . G A, 1008.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.599;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.114;PG=5,0,1,65,63,101;RAW_MQ=194196.00;ReadPosRankSum=0.182 GT:AD:DP:GQ:PL:PP:SB 0/1:45,37,0:82:99:1037,0,1601,1173,1712,2885:1042,0,1602,1238,1775,2986:25,20,18,19 +20 10000695 . G . . END=10000757 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:99:79:0,120,1800:0,184,1904 +20 10000758 . T A, 3838.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=270581.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,95,0:95:99:3867,286,0,3867,286,3867:3879,289,0,3936,349,3969:0,0,45,50 +20 10000759 . A . . END=10001018 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:99:52:0,120,1800:0,184,1904 +20 10001019 . T G, 650.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.541;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-7.498;PG=3,0,3,64,64,100;RAW_MQ=159195.00;ReadPosRankSum=-1.497 GT:AD:DP:GQ:PL:PP:SB 0/1:39,26,0:65:99:679,0,1426,796,1504,2300:682,0,1429,860,1568,2400:17,22,14,12 +20 10001020 . C . . END=10001297 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:46:0,117,1755:0,144,1854 +20 10001298 . T A, 2917.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=218493.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,73,0:73:99:2946,220,0,2946,220,2946:2959,223,0,3015,283,3048:0,0,41,32 +20 10001299 . C . . END=10001415 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:49:0,39,585:0,103,689 +20 10001416 . A . . END=10001422 GT:DP:GQ:MIN_DP:PL:PP 0/0:50:94:49:0,30,450:0,94,554 +20 10001423 . T . . END=10001426 GT:DP:GQ:MIN_DP:PL:PP 0/0:50:88:49:0,24,360:0,88,464 +20 10001427 . T . . END=10001427 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:69:53:0,5,1899:0,69,2003 +20 10001428 . T . . END=10001429 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:85:53:0,21,315:0,85,419 +20 10001430 . G . . END=10001431 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:64:56:0,0,1743:0,64,1847 +20 10001432 . A . . END=10001432 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:40:56:0,18,270:0,40,320 +20 10001433 . T . . END=10001433 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:64:56:0,0,1779:0,64,1883 +20 10001434 . G . . END=10001434 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:82:56:0,18,270:0,82,374 +20 10001435 . A . . END=10001435 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:64:55:0,0,1790:0,64,1894 +20 10001436 . A AAGGCT, 2301.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=56;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=11,3,0,68,63,102;RAW_MQ=93596.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,50,0:50:99:2339,156,0,2340,157,2340:2350,159,0,2408,220,2442:0,0,43,7 +20 10001437 . A . . END=10001437 GT:DP:GQ:MIN_DP:PL:PP 0/0:57:64:57:0,0,0:0,64,104 +20 10001438 . G . . END=10001473 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:99:51:0,118,1800:0,182,1904 +20 10001474 . C T, 2640.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=141456.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,73,0:73:99:2669,219,0,2669,219,2669:2681,222,0,2738,282,2771:0,0,48,25 +20 10001475 . G . . END=10001616 GT:DP:GQ:MIN_DP:PL:PP 0/0:95:99:72:0,120,1800:0,124,1815 +20 10001617 . C A, 1731.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.261;ClippingRankSum=0.000;DP=103;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.373;PG=5,0,1,65,63,101;RAW_MQ=358589.00;ReadPosRankSum=-0.578 GT:AD:DP:GQ:PL:PP:SB 0/1:52,51,0:103:99:1760,0,1781,1916,1935,3851:1765,0,1782,1981,1998,3952:23,29,33,18 +20 10001618 . T . . END=10001627 GT:DP:GQ:MIN_DP:PL:PP 0/0:101:99:95:0,120,1800:0,184,1904 +20 10001628 . G A, 3898.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=95;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,70,63,102;RAW_MQ=332548.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,95,0:95:99:3927,285,0,3927,285,3927:3940,288,0,3997,348,4029:0,0,55,40 +20 10001629 . G . . END=10001660 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:76:0,120,1800:0,184,1904 +20 10001661 . T C, 3606.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=275574.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,81,0:81:99:0|1:10001661_T_C:3635,249,0,3635,249,3635:3648,252,0,3704,312,3737:0,0,49,32 +20 10001662 . T . . END=10001669 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:82:0,120,1800:0,184,1904 +20 10001670 . T G, 3673.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=267297.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,81,0:81:99:0|1:10001661_T_C:3702,253,0,3702,253,3702:3715,256,0,3771,316,3804:0,0,46,35 +20 10001671 . G . . END=10002057 GT:DP:GQ:MIN_DP:PL:PP 0/0:76:99:57:0,120,1800:0,136,1837 +20 10002058 . T G, 2963.77 . AC=2,0;AF=1.00,0.00;AN=2;BaseQRankSum=1.931;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=3.068;PG=13,3,0,69,63,102;RAW_MQ=250206.00;ReadPosRankSum=-0.524 GT:AD:DP:GQ:PL:PP:SB 1/1:1,74,0:75:99:2992,216,0,2994,223,3001:3005,219,0,3063,286,3103:1,0,51,23 +20 10002059 . A . . END=10002098 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:65:0,120,1800:0,184,1904 +20 10002099 . C T, 1194.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.282;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.850;PG=0,5,16,63,71,103;RAW_MQ=209529.00;ReadPosRankSum=-0.360 GT:AD:DP:GQ:PL:PP:SB 0/1:27,38,0:65:99:1223,0,844,1304,958,2262:1218,0,855,1362,1024,2360:19,8,23,15 +20 10002100 . T . . END=10002137 GT:DP:GQ:MIN_DP:PL:PP 0/0:59:99:49:0,120,1800:0,184,1904 +20 10002138 . C G, 2443.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=168463.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,53,0:53:99:0|1:10002138_C_G:2472,169,0,2472,169,2472:2484,172,0,2541,232,2574:0,0,27,26 +20 10002139 . A . . END=10002141 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:99:52:0,120,1800:0,184,1904 +20 10002142 . G C, 2407.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=164863.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,52,0:52:99:0|1:10002138_C_G:2436,166,0,2436,166,2436:2448,169,0,2505,229,2538:0,0,24,28 +20 10002143 . T . . END=10002456 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:42:0,48,720:0,107,824 +20 10002457 . A . . END=10002457 GT:DP:GQ:MIN_DP:PL:PP 0/0:52:64:52:0,0,1572:0,64,1676 +20 10002458 . G GT,GTTT,GTTTTT, 2135.73 . AC=1,1,0,0;AF=0.500,0.500,0.00,0.00;AN=2;DP=47;ExcessHet=3.0103;MLEAC=1,1,0,0;MLEAF=0.500,0.500,0.00,0.00;PG=0,73,113,73,149,113,73,149,149,113,34,110,110,110,71;RAW_MQ=127415.00 GT:AD:DP:GQ:PL:PP:SB 1/2:0,6,6,4,0:16:9:2172,654,493,249,0,82,353,33,9,214,876,512,168,254,730:2023,578,457,173,0,46,277,33,9,178,761,473,129,215,652:0,0,12,4 +20 10002459 . T . . END=10002459 GT:DP:GQ:MIN_DP:PL:PP 0/0:59:64:59:0,0,1511:0,64,1615 +20 10002460 . T . . END=10002469 GT:DP:GQ:MIN_DP:PL:PP 0/0:63:99:61:0,72,1080:0,136,1184 +20 10002470 . C T, 2522.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=144226.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,61,0:61:99:2551,189,0,2551,189,2551:2563,192,0,2620,252,2653:0,0,34,27 +20 10002471 . T . . END=10002477 GT:DP:GQ:MIN_DP:PL:PP 0/0:64:99:63:0,84,1260:0,148,1364 +20 10002478 . A . . END=10002482 GT:DP:GQ:MIN_DP:PL:PP 0/0:52:64:46:0,0,731:0,64,835 +20 10002483 . A . . END=10002624 GT:DP:GQ:MIN_DP:PL:PP 0/0:38:99:33:0,72,1080:0,111,1184 +20 10002625 . G T, 2665.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=64;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=223179.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,64,0:64:99:2694,193,0,2694,193,2694:2706,196,0,2763,256,2796:0,0,26,38 +20 10002626 . G . . END=10003020 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:52:0,120,1800:0,137,1840 +20 10003021 . C T, 2383.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=60;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,70,63,102;RAW_MQ=208779.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,60,0:60:99:2412,181,0,2412,181,2412:2425,184,0,2482,244,2514:0,0,35,25 +20 10003022 . G . . END=10003121 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:39:0,81,1215:0,145,1319 +20 10003122 . C . . END=10003122 GT:DP:GQ:MIN_DP:PL:PP 0/0:47:49:47:0,37,1427:0,49,1457 +20 10003123 . A . . END=10003357 GT:DP:GQ:MIN_DP:PL:PP 0/0:88:99:55:0,120,1800:0,131,1828 +20 10003358 . A C, 1454.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.004;ClippingRankSum=0.000;DP=90;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.011;PG=5,0,1,65,63,101;RAW_MQ=321769.00;ReadPosRankSum=-0.444 GT:AD:DP:GQ:PL:PP:SB 0/1:45,44,0:89:99:1483,0,1477,1618,1609,3227:1488,0,1478,1683,1672,3328:31,14,29,15 +20 10003359 . C . . END=10003650 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:50:0,120,1800:0,129,1825 +20 10003651 . T C, 3620.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=93;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=325876.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,93,0:93:99:3649,279,0,3649,279,3649:3662,282,0,3718,342,3751:0,0,32,61 +20 10003652 . C . . END=10003691 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:70:0,120,1800:0,146,1858 +20 10003692 . A G, 2609.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=68;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=240338.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,68,0:68:99:2638,205,0,2638,205,2638:2651,208,0,2707,268,2740:0,0,25,43 +20 10003693 . T . . END=10003831 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:99:46:0,111,1665:0,133,1769 +20 10003832 . G A, 2705.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=215436.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,66,0:66:99:2734,199,0,2734,199,2734:2747,202,0,2803,262,2836:0,0,23,43 +20 10003833 . T . . END=10004093 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:99:43:0,108,1620:0,127,1724 +20 10004094 . A C, 1825.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=147492.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,53,0:53:99:1854,157,0,1854,157,1854:1867,160,0,1923,220,1956:0,0,35,18 +20 10004095 . C . . END=10004146 GT:DP:GQ:MIN_DP:PL:PP 0/0:52:99:45:0,109,1596:0,139,1700 +20 10004147 . A G, 1837.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=157262.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,52,0:52:99:1866,156,0,1866,156,1866:1878,159,0,1935,219,1968:0,0,21,31 +20 10004148 . G . . END=10004192 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:99:47:0,112,1687:0,176,1791 +20 10004193 . G T, 918.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.504;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.421;PG=0,17,41,64,84,104;RAW_MQ=186469.00;ReadPosRankSum=0.775 GT:AD:DP:GQ:PL:PP:SB 0/1:23,29,0:52:99:947,0,775,1016,860,1876:930,0,798,1063,927,1962:12,11,12,17 +20 10004194 . C . . END=10004221 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:99:49:0,72,1080:0,136,1184 +20 10004222 . C CA, 12.96 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=0.335;ClippingRankSum=0.000;DP=55;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.042;PG=0,72,112,12,88,30;RAW_MQ=198329.00;ReadPosRankSum=-0.052 GT:AD:DP:GQ:PL:PP:SB 0/0:31,8,0:39:22:50,0,923,153,952,1105:0,22,985,115,990,1085:18,13,4,4 +20 10004223 . A AG, 47.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.632;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.886;PG=0,13,31,64,79,103;RAW_MQ=214369.00;ReadPosRankSum=2.234 GT:AD:DP:GQ:PL:PP:SB 0/1:36,11,0:47:72:85,0,982,193,1017,1210:72,0,1001,244,1084,1301:16,20,5,6 +20 10004224 . A G, 0 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-0.383;ClippingRankSum=0.000;DP=67;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.609;PG=0,18,42,64,85,103;RAW_MQ=227310.00;ReadPosRankSum=1.728 GT:AD:DP:GQ:PL:PP:SB 0/0:48,3,0:51:99:0,95,1492,143,1500,1549:0,113,1534,207,1585,1652:20,28,2,1 +20 10004225 . A . . END=10004240 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:65:0,114,1710:0,137,1762 +20 10004241 . G . . END=10004241 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:64:66:0,0,1965:0,64,2069 +20 10004242 . A . . END=10004350 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:58:0,120,1800:0,139,1843 +20 10004351 . C G, 2755.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=243987.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,70,0:70:99:2784,211,0,2784,211,2784:2797,214,0,2853,274,2886:0,0,38,32 +20 10004352 . A . . END=10004388 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:62:0,120,1800:0,184,1904 +20 10004389 . T G, 2494.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=199570.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,62,0:62:99:2523,187,0,2523,187,2523:2536,190,0,2592,250,2625:0,0,25,37 +20 10004390 . G . . END=10004609 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:58:0,120,1800:0,140,1845 +20 10004610 . A C, 3625.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=89;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=306605.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,89,0:89:99:3654,267,0,3654,267,3654:3667,270,0,3723,330,3756:0,0,46,43 +20 10004611 . C . . END=10004724 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:99:64:0,120,1800:0,141,1848 +20 10004725 . A G, 951.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.154;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.008;PG=0,2,11,63,68,102;RAW_MQ=198562.00;ReadPosRankSum=1.791 GT:AD:DP:GQ:PL:PP:SB 0/1:35,30,0:65:99:980,0,1168,1085,1258,2343:978,0,1176,1145,1324,2442:10,25,17,13 +20 10004726 . T . . END=10004768 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:63:0,105,1575:0,169,1679 +20 10004769 . TAAAACTATGC T, 981.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.603;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.625;PG=0,5,15,63,71,103;RAW_MQ=216626.00;ReadPosRankSum=2.215 GT:AD:DP:GQ:PL:PP:SB 0/1:37,27,0:64:99:1019,0,1471,1130,1554,2684:1014,0,1482,1189,1620,2782:14,23,7,20 +20 10004780 . A . . END=10004780 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:64:70:0,0,795:0,64,899 +20 10004781 . A . . END=10004873 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:69:0,120,1800:0,184,1904 +20 10004874 . A C, 3602.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=87;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=20,7,0,74,64,103;RAW_MQ=306223.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,87,0:87:99:0|1:10004874_A_C:3631,261,0,3631,261,3631:3651,268,0,3705,325,3734:0,0,54,33 +20 10004875 . T . . END=10004886 GT:DP:GQ:MIN_DP:PL:PP 0/0:86:99:85:0,120,1800:0,148,1861 +20 10004887 . A G, 1323.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.356;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.067;PG=0,5,16,63,71,103;RAW_MQ=304923.00;ReadPosRankSum=-0.160 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:45,40,0:85:99:0|1:10004874_A_C:1352,0,1542,1487,1662,3149:1347,0,1553,1545,1728,3247:24,21,24,16 +20 10004888 . A . . END=10005009 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:65:0,120,1800:0,149,1863 +20 10005010 . C T, 2934.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=72;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=256441.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,72,0:72:99:2963,217,0,2963,217,2963:2976,220,0,3032,280,3065:0,0,44,28 +20 10005011 . G . . END=10005426 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:51:0,120,1800:0,135,1835 +20 10005427 . C T, 2214.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,70,63,102;RAW_MQ=195241.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,55,0:55:99:2243,165,0,2243,165,2243:2256,168,0,2313,228,2345:0,0,27,28 +20 10005428 . A . . END=10005498 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:58:0,120,1800:0,130,1826 +20 10005499 . A G, 3053.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=273600.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,76,0:76:99:3082,229,0,3082,229,3082:3095,232,0,3151,292,3184:0,0,45,31 +20 10005500 . T . . END=10005586 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:66:0,120,1800:0,184,1904 +20 10005587 . A G, 1229.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.834;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.972;PG=5,0,1,65,63,101;RAW_MQ=257810.00;ReadPosRankSum=0.649 GT:AD:DP:GQ:PL:PP:SB 0/1:36,36,0:72:99:1258,0,1236,1366,1345,2710:1263,0,1237,1431,1408,2811:19,17,16,20 +20 10005588 . A . . END=10005722 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:73:0,120,1800:0,184,1904 +20 10005723 . A G, 3062.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=86;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=307369.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,86,0:86:99:3091,258,0,3091,258,3091:3104,261,0,3160,321,3193:0,0,48,38 +20 10005724 . A . . END=10006290 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:53:0,120,1800:0,141,1848 +20 10006291 . G A, 978.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.311;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.081;PG=1,0,5,63,65,101;RAW_MQ=295179.00;ReadPosRankSum=-1.614 GT:AD:DP:GQ:PL:PP:SB 0/1:53,31,0:84:99:1007,0,1905,1167,1998,3165:1008,0,1910,1230,2063,3266:25,28,16,15 +20 10006292 . A . . END=10006403 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:76:0,120,1800:0,184,1904 +20 10006404 . A C, 2928.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=269451.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,76,0:76:99:2957,228,0,2957,228,2957:2970,231,0,3026,291,3059:0,0,27,49 +20 10006405 . C . . END=10006681 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:65:0,120,1800:0,139,1844 +20 10006682 . T A, 2874.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=257810.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,73,0:73:99:2903,219,0,2903,219,2903:2916,222,0,2972,282,3005:0,0,44,29 +20 10006683 . A . . END=10006816 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:61:0,45,675:0,109,779 +20 10006817 . A . . END=10006818 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:94:77:0,30,450:0,94,554 +20 10006819 . AAAAC A, 2531.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=76;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=11,3,0,23,17,40;RAW_MQ=284000.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,58,0:58:99:2569,176,0,2569,176,2569:2580,179,0,2592,193,2609:0,0,30,28 +20 10006824 . A . . END=10006824 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:64:75:0,0,0:0,64,104 +20 10006825 . A . . END=10007149 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:59:0,120,1800:0,129,1823 +20 10007150 . G C, 669.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-4.476;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,5,17,63,72,103;RAW_MQ=226800.00;ReadPosRankSum=-1.745 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:38,25,0:63:99:0|1:10007150_G_C:698,0,1479,813,1554,2366:693,0,1490,871,1620,2464:16,22,14,11 +20 10007151 . G . . END=10007174 GT:DP:GQ:MIN_DP:PL:PP 0/0:57:99:56:0,120,1800:0,184,1904 +20 10007175 . C T, 1350.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.249;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.319;PG=1,0,5,63,65,101;RAW_MQ=216841.00;ReadPosRankSum=-0.730 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:23,38,0:61:99:1|0:10007150_G_C:1379,0,780,1448,894,2343:1380,0,785,1511,959,2444:9,14,18,20 +20 10007176 . T . . END=10007351 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:99:47:0,119,1671:0,183,1775 +20 10007352 . C T, 2764.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=249241.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,69,0:69:99:2793,208,0,2793,208,2793:2806,211,0,2862,271,2895:0,0,29,40 +20 10007353 . A . . END=10007530 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:99:58:0,120,1800:0,129,1824 +20 10007531 . A G, 2920.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=260569.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,72,0:72:99:2949,217,0,2949,217,2949:2962,220,0,3018,280,3051:0,0,48,24 +20 10007532 . G . . END=10007979 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:65:0,120,1800:0,124,1815 +20 10007980 . A C, 3524.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=90;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=331800.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,90,0:90:99:3553,270,0,3553,270,3553:3565,273,0,3622,333,3655:0,0,39,51 +20 10007981 . A . . END=10008021 GT:DP:GQ:MIN_DP:PL:PP 0/0:86:99:81:0,54,810:0,118,914 +20 10008022 . A . . END=10008023 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:97:85:0,33,495:0,97,599 +20 10008024 . A . . END=10008028 GT:DP:GQ:MIN_DP:PL:PP 0/0:87:73:86:0,9,135:0,73,239 +20 10008029 . T TA, 1986.73 . AC=2,0;AF=1.00,0.00;AN=2;BaseQRankSum=0.409;ClippingRankSum=0.000;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.576;PG=9,2,0,12,7,21;RAW_MQ=327251.00;ReadPosRankSum=-1.055 GT:AD:DP:GQ:PL:PP:SB 1/1:3,72,0:75:99:2024,145,0,2033,222,2110:2033,147,0,2045,229,2131:1,2,27,45 +20 10008030 . A . . END=10008030 GT:DP:GQ:MIN_DP:PL:PP 0/0:91:64:91:0,0,0:0,64,104 +20 10008031 . A . . END=10008135 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:76:0,48,720:0,112,824 +20 10008136 . A . . END=10008140 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:82:76:0,18,270:0,82,374 +20 10008141 . C . . END=10008142 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:70:77:0,6,90:0,70,194 +20 10008143 . C . . END=10008145 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:67:76:0,3,45:0,67,149 +20 10008146 . TA T, 2141.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=268000.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,70,0:70:99:2179,211,0,2179,211,2179:2192,214,0,2248,274,2281:0,0,38,32 +20 10008148 . A . . END=10008148 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:64:74:0,0,0:0,64,104 +20 10008149 . A . . END=10008220 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:74:0,120,1800:0,138,1842 +20 10008221 . T C, 3224.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=80;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=289669.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,80,0:80:99:3253,240,0,3253,240,3253:3266,243,0,3322,303,3355:0,0,43,37 +20 10008222 . T . . END=10008457 GT:DP:GQ:MIN_DP:PL:PP 0/0:64:99:45:0,108,1620:0,128,1724 +20 10008458 . T G, 2654.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=193211.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,69,0:69:99:2683,207,0,2683,207,2683:2696,210,0,2752,270,2785:0,0,30,39 +20 10008459 . A . . END=10008741 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:40:0,78,1170:0,130,1274 +20 10008742 . G T, 715.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.893;ClippingRankSum=0.000;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.502;PG=0,5,16,63,71,102;RAW_MQ=67874.00;ReadPosRankSum=0.772 GT:AD:DP:GQ:PL:PP:SB 0/1:23,26,0:49:99:744,0,580,813,658,1471:739,0,591,871,724,1568:10,13,11,15 +20 10008743 . T . . END=10008750 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:99:47:0,51,765:0,115,869 +20 10008751 . A . . END=10008754 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:94:49:0,30,450:0,94,554 +20 10008755 . A . . END=10008755 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:99:51:0,36,540:0,100,644 +20 10008756 . T . . END=10008756 GT:DP:GQ:MIN_DP:PL:PP 0/0:45:97:45:0,33,495:0,97,599 +20 10008757 . A . . END=10008757 GT:DP:GQ:MIN_DP:PL:PP 0/0:48:88:48:0,24,360:0,88,464 +20 10008758 . C CA, 684.14 . AC=2,0;AF=1.00,0.00;AN=2;BaseQRankSum=0.130;ClippingRankSum=0.000;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=-1.168;PG=3,0,3,11,11,24;RAW_MQ=54656.00;ReadPosRankSum=-0.234 GT:AD:DP:GQ:PL:PP:SB 1/1:4,31,0:35:7:721,10,0,733,102,825:721,7,0,741,110,846:3,1,16,15 +20 10008759 . A . . END=10008759 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:64:55:0,0,0:0,64,104 +20 10008760 . A . . END=10008772 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:53:0,120,1800:0,184,1904 +20 10008773 . T . . END=10008773 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:64:54:0,0,1660:0,64,1764 +20 10008774 . T . . END=10008920 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:45:0,60,990:0,124,1094 +20 10008921 . C CA, 253.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.610;ClippingRankSum=0.000;DP=49;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.906;PG=0,1,9,13,18,33;RAW_MQ=155512.00;ReadPosRankSum=-0.415 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:290,0,373,357,431,792:10,8,8,8 +20 10008922 . A . . END=10008922 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:64:51:0,0,714:0,64,818 +20 10008923 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:48:0,66,990:0,130,1094 +20 10008948 . TA T, 2057.73 . AC=2,0;AF=1.00,0.00;AN=2;BaseQRankSum=0.994;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;PG=12,3,0,69,63,102;RAW_MQ=139463.00;ReadPosRankSum=0.749 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:2107,110,0,2167,222,2252:1,0,35,15 +20 10008950 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL:PP 0/0:48:64:48:0,0,0:0,64,104 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1666.73 . AC=0,1,0,1,0;AF=0.00,0.500,0.00,0.500,0.00;AN=2;BaseQRankSum=0.941;ClippingRankSum=0.000;DP=60;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;PG=0,72,112,5,80,15,72,148,80,112,72,148,80,148,112,13,88,21,88,88,32;RAW_MQ=154909.00;ReadPosRankSum=0.685 GT:AD:DP:GQ:PL:PP:SB 2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,780,607,1321:1624,868,1290,450,811,780,718,582,173,735,574,410,0,511,562,1068,1100,685,788,615,1273:1,0,25,8 +20 10008966 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL:PP 0/0:60:99:38:0,94,1530:0,158,1634 +20 10009227 . A G, 1369.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.220;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.428;PG=0,5,16,63,71,103;RAW_MQ=202588.00;ReadPosRankSum=-1.093 GT:AD:DP:GQ:PL:PP:SB 0/1:23,39,0:62:99:1398,0,740,1468,857,2325:1393,0,751,1526,923,2423:16,7,19,20 +20 10009228 . G . . END=10009245 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:99:59:0,120,1800:0,184,1904 +20 10009246 . A G, 3002.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=20,7,0,74,64,103;RAW_MQ=242208.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,77,0:77:99:3031,231,0,3031,231,3031:3051,238,0,3105,295,3134:0,0,42,35 +20 10009247 . A . . END=10009399 GT:DP:GQ:MIN_DP:PL:PP 0/0:86:99:68:0,120,1800:0,141,1848 +20 10009400 . T A, 2998.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=266400.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,74,0:74:99:3027,223,0,3027,223,3027:3040,226,0,3096,286,3129:0,0,39,35 +20 10009401 . A . . END=10009511 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:72:0,120,1800:0,184,1904 +20 10009512 . C G, 3039.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=263240.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,77,0:77:99:3068,231,0,3068,231,3068:3081,234,0,3137,294,3170:0,0,30,47 +20 10009513 . A . . END=10009718 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:63:0,120,1800:0,139,1844 +20 10009719 . A G, 1895.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=8,1,0,67,63,101;RAW_MQ=207410.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,59,0:59:99:1924,175,0,1924,175,1924:1932,176,0,1991,238,2025:0,0,26,33 +20 10009720 . T . . END=10009794 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:99:47:0,120,1800:0,138,1842 +20 10009795 . A G, 1880.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=47;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,102;RAW_MQ=166969.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,47,0:47:99:1909,141,0,1909,141,1909:1921,144,0,1978,204,2011:0,0,16,31 +20 10009796 . C . . END=10009832 GT:DP:GQ:MIN_DP:PL:PP 0/0:49:99:44:0,63,945:0,127,1049 +20 10009833 . A . . END=10009841 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:91:53:0,27,405:0,91,509 +20 10009842 . G GAA, 532.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.872;ClippingRankSum=0.000;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.603;PG=0,16,37,64,83,104;RAW_MQ=150092.00;ReadPosRankSum=0.052 GT:AD:DP:GQ:PL:PP:SB 0/1:19,15,0:34:99:570,0,690,629,738,1367:554,0,712,677,805,1455:9,10,8,7 +20 10009843 . A . . END=10009843 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:46:56:0,27,405:0,46,449 +20 10009844 . G A, 661.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.048;ClippingRankSum=0.000;DP=51;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.975;PG=0,5,17,63,72,103;RAW_MQ=147168.00;ReadPosRankSum=0.259 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:685,0,597,797,710,1479:8,8,9,10 +20 10009845 . A . . END=10009845 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:49:55:0,30,450:0,49,494 +20 10009846 . G . . END=10009847 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:94:55:0,30,450:0,94,554 +20 10009848 . G . . END=10009870 GT:DP:GQ:MIN_DP:PL:PP 0/0:60:99:56:0,39,585:0,103,689 +20 10009871 . A G, 658.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.803;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.495;PG=0,4,14,63,70,102;RAW_MQ=158337.00;ReadPosRankSum=1.572 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:683,0,604,798,718,1489:10,7,9,10 +20 10009872 . G . . END=10009874 GT:DP:GQ:MIN_DP:PL:PP 0/0:58:99:55:0,96,1440:0,160,1544 +20 10009875 . A G,AGGGAGG, 2369.73 . AC=1,1,0;AF=0.500,0.500,0.00;AN=2;BaseQRankSum=0.378;ClippingRankSum=0.000;DP=58;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;MQRankSum=1.361;PG=0,2,10,72,77,111,63,68,138,102;RAW_MQ=147537.00;ReadPosRankSum=-0.083 GT:AD:DP:GQ:PL:PP:SB 1/2:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2330,570,466,692,0,608,1867,646,761,1830:2,0,12,16 +20 10009876 . G . . END=10009878 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:55:0,85,1620:0,149,1724 +20 10009879 . A G, 2244.77 . AC=2,0;AF=1.00,0.00;AN=2;BaseQRankSum=1.534;ClippingRankSum=0.000;DP=50;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=1.570;PG=2,0,4,63,64,101;RAW_MQ=124261.00;ReadPosRankSum=1.391 GT:AD:DP:GQ:PL:PP:SB 1/1:2,47,0:49:99:2273,150,0,2276,154,2279:2270,146,0,2335,214,2375:2,0,15,32 +20 10009880 . G . . END=10009882 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:99:50:0,80,1755:0,144,1859 +20 10009883 . A G, 2151.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=50;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=7,0,0,66,62,101;RAW_MQ=132938.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,47,0:47:99:2180,147,0,2180,147,2181:2187,147,0,2246,209,2282:0,0,15,32 +20 10009884 . G . . END=10009885 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:99:52:0,58,1739:0,122,1843 +20 10009886 . A . . END=10009886 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:64:53:0,0,1490:0,64,1594 +20 10009887 . G . . END=10009887 GT:DP:GQ:MIN_DP:PL:PP 0/0:50:99:50:0,109,1906:0,173,2010 +20 10009888 . A . . END=10009888 GT:DP:GQ:MIN_DP:PL:PP 0/0:51:64:51:0,0,1610:0,64,1714 +20 10009889 . A . . END=10010392 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:45:0,44,1665:0,108,1769 +20 10010393 . T G, 1464.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.351;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.284;PG=0,5,16,63,71,103;RAW_MQ=278882.00;ReadPosRankSum=-1.630 GT:AD:DP:GQ:PL:PP:SB 0/1:36,43,0:79:99:1493,0,1230,1601,1359,2961:1488,0,1241,1659,1425,3059:24,12,19,24 +20 10010394 . T . . END=10010532 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:67:0,39,585:0,103,689 +20 10010533 . G . . END=10010533 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:97:83:0,33,495:0,97,599 +20 10010534 . A . . END=10010534 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:88:84:0,24,360:0,88,464 +20 10010535 . A . . END=10010535 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:76:85:0,12,180:0,76,284 +20 10010536 . G GA, 2462.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=85;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=322900.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,79,0:79:99:2500,243,0,2500,244,2500:2513,246,0,2569,307,2602:0,0,36,43 +20 10010537 . A . . END=10010537 GT:DP:GQ:MIN_DP:PL:PP 0/0:88:64:88:0,0,0:0,64,104 +20 10010538 . A . . END=10010765 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:68:0,120,1800:0,184,1904 +20 10010766 . T G, 2411.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=67;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=241200.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,66,0:66:99:2440,199,0,2440,199,2440:2453,202,0,2509,262,2542:0,0,35,31 +20 10010767 . G . . END=10010831 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:99:61:0,120,1800:0,184,1904 +20 10010832 . T C, 2951.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=75;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=265538.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,75,0:75:99:2980,226,0,2980,226,2980:2993,229,0,3049,289,3082:0,0,31,44 +20 10010833 . A . . END=10011074 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:99:73:0,120,1800:0,136,1839 +20 10011075 . C T, 1325.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.364;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=4,0,2,65,63,101;RAW_MQ=306000.00;ReadPosRankSum=-1.057 GT:AD:DP:GQ:PL:PP:SB 0/1:44,39,0:83:99:1354,0,1333,1485,1450,2935:1358,0,1335,1550,1513,3036:22,22,22,17 +20 10011076 . G . . END=10011308 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:99:52:0,120,1800:0,141,1849 +20 10011309 . T C, 2692.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=277200.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,77,0:77:99:2721,231,0,2721,231,2721:2734,234,0,2790,294,2823:0,0,30,47 +20 10011310 . G . . END=10011516 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:70:0,120,1800:0,138,1842 +20 10011517 . GAA G,GA,GAAA, 490.73 . AC=0,1,0,0;AF=0.00,0.500,0.00,0.00;AN=2;BaseQRankSum=0.690;ClippingRankSum=0.000;DP=91;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=1.797;PG=1,13,31,0,15,5,19,34,21,43,63,78,65,84,101;RAW_MQ=326510.00;ReadPosRankSum=1.154 GT:AD:DP:GQ:PL:PP:SB 0/2:37,2,28,6,0:73:99:528,611,2120,0,1042,875,604,1499,722,1648,667,1700,966,1470,1638:529,624,2151,0,1057,880,623,1533,743,1691,730,1778,1031,1554,1739:23,14,19,17 +20 10011520 . A . . END=10011665 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:62:0,120,1800:0,142,1850 +20 10011666 . C T, 2961.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=254523.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,73,0:73:99:2990,220,0,2990,220,2990:3003,223,0,3059,283,3092:0,0,43,30 +20 10011667 . A . . END=10011938 GT:DP:GQ:MIN_DP:PL:PP 0/0:87:99:64:0,111,1665:0,144,1769 +20 10011939 . C T, 2469.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=61;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=193043.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,61,0:61:99:2498,184,0,2498,184,2498:2511,187,0,2567,247,2600:0,0,23,38 +20 10011940 . G . . END=10011944 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:99:54:0,114,1710:0,178,1814 +20 10011945 . G . . END=10011945 GT:DP:GQ:MIN_DP:PL:PP 0/0:50:94:50:0,84,1730:0,94,1756 +20 10011946 . T . . END=10012007 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:99:44:0,36,540:0,100,644 +20 10012008 . G . . END=10012010 GT:DP:GQ:MIN_DP:PL:PP 0/0:64:97:63:0,33,495:0,97,599 +20 10012011 . T . . END=10012013 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:82:65:0,18,270:0,82,374 +20 10012014 . A . . END=10012015 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:73:66:0,9,135:0,73,239 +20 10012016 . T . . END=10012020 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:64:68:0,0,0:0,64,104 +20 10012021 . CA C, 1975.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=228076.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,66,0:66:99:2013,198,0,2013,198,2013:2026,201,0,2082,261,2115:0,0,26,40 +20 10012023 . A . . END=10012023 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:64:69:0,0,0:0,64,104 +20 10012024 . A . . END=10012233 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:25:0,53,990:0,99,1094 +20 10012234 . G . . END=10012234 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:92:25:0,69,1035:0,92,1087 +20 10012235 . A . . END=10012253 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:99:24:0,48,893:0,112,997 +20 10012254 . A . . END=10012254 GT:DP:GQ:MIN_DP:PL:PP 0/0:24:71:24:0,57,865:0,71,899 +20 10012255 . C . . END=10012280 GT:DP:GQ:MIN_DP:PL:PP 0/0:27:99:23:0,58,900:0,122,1004 +20 10012281 . C . . END=10012281 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:86:25:0,69,1035:0,86,1075 +20 10012282 . T . . END=10012349 GT:DP:GQ:MIN_DP:PL:PP 0/0:26:99:23:0,58,884:0,122,988 +20 10012350 . G . . END=10012350 GT:DP:GQ:MIN_DP:PL:PP 0/0:23:89:23:0,63,945:0,89,1002 +20 10012351 . G . . END=10012361 GT:DP:GQ:MIN_DP:PL:PP 0/0:24:99:23:0,48,720:0,112,824 +20 10012362 . G T, 835.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=23;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=7,1,0,11,7,20;RAW_MQ=66527.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,23,0:23:70:864,69,0,864,69,864:871,70,0,875,76,884:0,0,2,21 +20 10012363 . G . . END=10012371 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:99:19:0,51,765:0,115,869 +20 10012372 . G . . END=10012372 GT:DP:GQ:MIN_DP:PL:PP 0/0:19:69:19:0,54,810:0,69,847 +20 10012373 . G . . END=10012383 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:99:17:0,39,585:0,103,689 +20 10012384 . T C, 229.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.773;ClippingRankSum=0.000;DP=19;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.811;PG=3,0,3,64,64,101;RAW_MQ=54886.00;ReadPosRankSum=0.190 GT:AD:DP:GQ:PL:PP:SB 0/1:10,8,0:18:99:258,0,355,288,379,667:261,0,358,352,443,768:0,10,2,6 +20 10012385 . T . . END=10012386 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:99:17:0,39,585:0,103,689 +20 10012387 . T C, 533.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=17;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=11,2,0,68,63,102;RAW_MQ=47686.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,16,0:16:52:562,50,0,562,50,562:573,52,0,630,113,664:0,0,2,14 +20 10012388 . G . . END=10012402 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:99:13:0,36,540:0,100,644 +20 10012403 . T . . END=10012403 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:81:15:0,17,521:0,81,625 +20 10012404 . G . . END=10012405 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:99:14:0,39,564:0,103,668 +20 10012406 . C . . END=10012407 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:66:15:0,2,396:0,66,500 +20 10012408 . G . . END=10012409 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:99:15:0,39,585:0,103,689 +20 10012410 . C . . END=10012412 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:94:14:0,30,450:0,94,554 +20 10012413 . C . . END=10012413 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:55:16:0,33,495:0,55,545 +20 10012414 . G . . END=10012416 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:97:14:0,33,495:0,97,599 +20 10012417 . C . . END=10012476 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:99:13:0,36,482:0,100,586 +20 10012477 . G . . END=10012478 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:97:17:0,33,495:0,97,599 +20 10012479 . A G, 592.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=17;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=11,2,0,67,62,100;RAW_MQ=45990.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,17,0:17:52:0|1:10012479_A_G:621,50,0,621,50,621:632,52,0,688,112,721:0,0,9,8 +20 10012480 . G . . END=10012482 GT:DP:GQ:MIN_DP:PL:PP 0/0:17:88:16:0,24,360:0,88,464 +20 10012483 . G . . END=10012485 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:91:13:0,27,405:0,91,509 +20 10012486 . G . . END=10012486 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:52:14:0,27,405:0,52,461 +20 10012487 . A . . END=10012489 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:12:0,27,405:0,91,509 +20 10012490 . G . . END=10012491 GT:DP:GQ:MIN_DP:PL:PP 0/0:10:86:8:0,22,269:0,86,373 +20 10012492 . G . . END=10012494 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:91:9:0,27,304:0,91,408 +20 10012495 . C . . END=10012495 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:58:11:0,30,450:0,58,511 +20 10012496 . T . . END=10012497 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:94:11:0,30,450:0,94,554 +20 10012498 . C G, 466.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=11;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,68,62,100;RAW_MQ=22302.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,11,0:11:36:0|1:10012479_A_G:495,33,0,495,33,495:507,36,0,563,95,595:0,0,4,7 +20 10012499 . G . . END=10012503 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:10:0,27,350:0,91,454 +20 10012504 . C . . END=10012508 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:88:10:0,24,360:0,88,464 +20 10012509 . A . . END=10012513 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:94:11:0,30,450:0,94,554 +20 10012514 . C . . END=10012514 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:88:11:0,24,360:0,88,464 +20 10012515 . A . . END=10012515 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:12:0,27,405:0,91,509 +20 10012516 . G . . END=10012517 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:88:11:0,24,360:0,88,464 +20 10012518 . T C, 406.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=9;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=10,2,0,67,62,100;RAW_MQ=15102.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,9,0:9:32:0|1:10012479_A_G:435,30,0,435,30,435:445,32,0,502,92,535:0,0,4,5 +20 10012519 . C . . END=10012519 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:12:0,27,405:0,91,509 +20 10012520 . A . . END=10012520 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:88:12:0,24,400:0,88,504 +20 10012521 . C T, 46.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.362;ClippingRankSum=0.000;DP=11;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.038;PG=4,0,2,63,63,99;RAW_MQ=19192.00;ReadPosRankSum=1.973 GT:AD:DP:GQ:PL:PP:SB 0/1:8,3,0:11:79:75,0,224,99,233,332:79,0,226,162,296,431:4,4,2,1 +20 10012522 . A . . END=10012526 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:10:0,27,405:0,91,509 +20 10012527 . C . . END=10012541 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:82:8:0,18,270:0,82,374 +20 10012542 . C . . END=10012544 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:79:8:0,15,225:0,79,329 +20 10012545 . C . . END=10012545 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:39:8:0,12,180:0,39,239 +20 10012546 . G . . END=10012557 GT:DP:GQ:MIN_DP:PL:PP 0/0:10:70:6:0,6,90:0,70,194 +20 10012558 . C . . END=10012569 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:64:8:0,0,0:0,64,104 +20 10012570 . G GCA, 457.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=10;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=10,2,0,67,62,100;RAW_MQ=13361.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,9,0:9:35:0|1:10012570_G_GCA:495,33,0,495,33,495:505,35,0,562,95,595:0,0,8,1 +20 10012571 . G . . END=10012571 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:64:11:0,0,0:0,64,104 +20 10012572 . GT G, 457.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=12;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=10,2,0,67,62,100;RAW_MQ=17802.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,11,0:11:35:0|1:10012570_G_GCA:495,33,0,495,33,495:505,35,0,562,95,595:0,0,10,1 +20 10012574 . G . . END=10012576 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:64:12:0,0,0:0,64,104 +20 10012577 . C . . END=10012577 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:73:12:0,9,419:0,73,523 +20 10012578 . G . . END=10012578 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:66:12:0,2,328:0,66,432 +20 10012579 . G . . END=10012581 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:97:12:0,33,495:0,97,599 +20 10012582 . C . . END=10012587 GT:DP:GQ:MIN_DP:PL:PP 0/0:13:99:13:0,36,540:0,100,644 +20 10012588 . G . . END=10012589 GT:DP:GQ:MIN_DP:PL:PP 0/0:13:97:12:0,33,495:0,97,599 +20 10012590 . C . . END=10012591 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:99:14:0,36,540:0,100,644 +20 10012592 . G . . END=10012592 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:78:14:0,14,377:0,78,481 +20 10012593 . C . . END=10012595 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:99:14:0,36,540:0,100,644 +20 10012596 . T . . END=10012618 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:91:14:0,27,405:0,91,509 +20 10012619 . T . . END=10012627 GT:DP:GQ:MIN_DP:PL:PP 0/0:19:85:17:0,21,315:0,85,419 +20 10012628 . G . . END=10012628 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:49:21:0,24,360:0,49,415 +20 10012629 . T . . END=10012630 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:88:21:0,24,360:0,88,464 +20 10012631 . C CG, 484.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.030;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.670;PG=0,3,12,62,68,101;RAW_MQ=49690.00;ReadPosRankSum=-0.835 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:8,13,0:21:99:0|1:10012631_C_CG:522,0,297,546,336,882:519,0,306,605,401,980:8,0,9,4 +20 10012632 . G . . END=10012632 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:64:21:0,0,0:0,64,104 +20 10012633 . C . . END=10012634 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:99:20:0,35,707:0,99,811 +20 10012635 . C . . END=10012635 GT:DP:GQ:MIN_DP:PL:PP 0/0:22:77:22:0,54,810:0,77,861 +20 10012636 . G C, 527.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.711;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.513;PG=0,3,11,62,68,101;RAW_MQ=52665.00;ReadPosRankSum=-0.718 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:8,14,0:22:99:0|1:10012631_C_CG:556,0,294,580,336,916:553,0,303,640,401,1014:8,0,10,4 +20 10012637 . A . . END=10012713 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:99:20:0,54,810:0,118,914 +20 10012714 . G C, 1300.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=35;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,101;RAW_MQ=98462.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,35,0:35:99:1329,105,0,1329,105,1329:1341,108,0,1398,168,1430:0,0,29,6 +20 10012715 . C . . END=10012750 GT:DP:GQ:MIN_DP:PL:PP 0/0:36:99:27:0,69,1035:0,133,1139 +20 10012751 . T C, 937.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=33;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=12,3,0,69,63,101;RAW_MQ=81069.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,30,0:30:92:966,89,0,966,89,966:978,92,0,1035,152,1067:0,0,17,13 +20 10012752 . C . . END=10013118 GT:DP:GQ:MIN_DP:PL:PP 0/0:43:99:28:0,69,908:0,99,1012 +20 10013119 . C T, 1011.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.724;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.089;PG=0,4,13,63,70,102;RAW_MQ=156381.00;ReadPosRankSum=0.336 GT:AD:DP:GQ:PL:PP:SB 0/1:29,30,0:59:99:1040,0,936,1127,1026,2153:1036,0,946,1186,1092,2252:19,10,17,13 +20 10013120 . A . . END=10013573 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:99:52:0,120,1800:0,136,1838 +20 10013574 . G A, 1050.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.469;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.271;PG=4,0,2,64,63,101;RAW_MQ=236198.00;ReadPosRankSum=0.789 GT:AD:DP:GQ:PL:PP:SB 0/1:38,31,0:69:99:1079,0,1301,1194,1394,2588:1083,0,1303,1258,1457,2689:15,23,7,24 +20 10013575 . T . . END=10014989 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:42:0,93,1625:0,131,1729 +20 10014990 . C CAT, 1237.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.930;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=3.107;PG=5,0,1,65,63,101;RAW_MQ=321369.00;ReadPosRankSum=-0.343 GT:AD:DP:GQ:PL:PP:SB 0/1:38,38,0:76:99:1275,0,1248,1389,1365,2755:1280,0,1249,1454,1428,2856:28,10,25,13 +20 10014991 . A . . END=10014991 GT:DP:GQ:MIN_DP:PL:PP 0/0:88:64:88:0,0,402:0,64,506 +20 10014992 . T . . END=10015535 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:20:0,38,675:0,102,779 +20 10015536 . G . . END=10015540 GT:DP:GQ:MIN_DP:PL:PP 0/0:20:97:18:0,33,495:0,97,599 +20 10015541 . G . . END=10015541 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:61:18:0,33,495:0,61,555 +20 10015542 . G . . END=10015546 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:97:15:0,33,495:0,97,599 +20 10015547 . G . . END=10015547 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:30:15:0,24,360:0,30,377 +20 10015548 . G . . END=10015552 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:64:11:0,0,0:0,64,104 +20 10015553 . A . . END=10015553 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:26:11:0,0,0:0,26,58 +20 10015554 . G . . END=10015557 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:64:11:0,0,0:0,64,104 +20 10015558 . G . . END=10015558 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:10:9:0,0,0:0,10,26 +20 10015559 . A . . END=10015559 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:64:8:0,0,0:0,64,104 +20 10015560 . G . . END=10015560 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:12:8:0,0,0:0,12,30 +20 10015561 . G . . END=10015561 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:64:8:0,0,0:0,64,104 +20 10015562 . C . . END=10015562 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:23:8:0,0,0:0,23,52 +20 10015563 . G . . END=10015567 GT:DP:GQ:MIN_DP:PL:PP 0/0:7:64:6:0,0,0:0,64,104 +20 10015568 . C . . END=10015568 GT:DP:GQ:MIN_DP:PL:PP 0/0:7:26:7:0,3,45:0,26,97 +20 10015569 . G . . END=10015580 GT:DP:GQ:MIN_DP:PL:PP 0/0:5:67:5:0,3,45:0,67,149 +20 10015581 . G . . END=10015582 GT:DP:GQ:MIN_DP:PL:PP 0/0:6:70:6:0,6,90:0,70,194 +20 10015583 . A . . END=10015583 GT:DP:GQ:MIN_DP:PL:PP 0/0:6:31:6:0,6,90:0,31,145 +20 10015584 . G . . END=10015610 GT:DP:GQ:MIN_DP:PL:PP 0/0:4:70:2:0,6,69:0,70,173 +20 10015611 . C . . END=10015616 GT:DP:GQ:MIN_DP:PL:PP 0/0:6:82:6:0,18,193:0,82,297 +20 10015617 . A . . END=10015632 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:91:9:0,27,254:0,91,358 +20 10015633 . T . . END=10015637 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:99:12:0,36,471:0,100,575 +20 10015638 . C . . END=10015641 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:97:12:0,33,495:0,97,599 +20 10015642 . C . . END=10015661 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:99:13:0,36,540:0,100,644 +20 10015662 . G . . END=10015678 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:11:0,27,405:0,91,509 +20 10015679 . C T, 140.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.200;ClippingRankSum=0.000;DP=11;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,3,13,62,68,100;RAW_MQ=39600.00;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL:PP:SB 0/1:5,5,0:10:99:169,0,166,184,181,365:166,0,175,242,246,461:5,0,5,0 +20 10015680 . G . . END=10015687 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:91:11:0,27,405:0,91,509 +20 10015688 . C . . END=10015688 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:61:11:0,33,400:0,61,461 +20 10015689 . G . . END=10015693 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:94:10:0,30,292:0,94,396 +20 10015694 . C . . END=10015694 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:87:12:0,23,389:0,87,493 +20 10015695 . C . . END=10015697 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:12:0,27,405:0,91,509 +20 10015698 . C . . END=10015698 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:87:12:0,23,401:0,87,505 +20 10015699 . C . . END=10015708 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:91:11:0,27,405:0,91,509 +20 10015709 . C . . END=10015714 GT:DP:GQ:MIN_DP:PL:PP 0/0:13:99:13:0,36,540:0,100,644 +20 10015715 . C . . END=10015716 GT:DP:GQ:MIN_DP:PL:PP 0/0:13:97:13:0,33,495:0,97,599 +20 10015717 . T . . END=10015723 GT:DP:GQ:MIN_DP:PL:PP 0/0:13:99:13:0,36,540:0,100,644 +20 10015724 . G . . END=10015725 GT:DP:GQ:MIN_DP:PL:PP 0/0:13:97:12:0,33,495:0,97,599 +20 10015726 . G . . END=10015726 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:85:12:0,21,330:0,85,434 +20 10015727 . C . . END=10015728 GT:DP:GQ:MIN_DP:PL:PP 0/0:14:99:14:0,39,585:0,103,689 +20 10015729 . C . . END=10015729 GT:DP:GQ:MIN_DP:PL:PP 0/0:15:46:15:0,42,630:0,46,644 +20 10015730 . G . . END=10015760 GT:DP:GQ:MIN_DP:PL:PP 0/0:19:99:15:0,39,558:0,103,662 +20 10015761 . T C, 344.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.982;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.294;PG=4,0,2,64,63,99;RAW_MQ=76441.00;ReadPosRankSum=-0.425 GT:AD:DP:GQ:PL:PP:SB 0/1:9,13,0:22:99:373,0,284,400,323,723:377,0,286,464,386,822:9,0,12,1 +20 10015762 . A . . END=10015762 GT:DP:GQ:MIN_DP:PL:PP 0/0:22:91:22:0,66,857:0,91,912 +20 10015763 . C . . END=10018157 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:99:23:0,63,839:0,99,943 +20 10018158 . G C, 1639.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.213;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.118;PG=4,0,2,65,63,101;RAW_MQ=318169.00;ReadPosRankSum=0.516 GT:AD:DP:GQ:PL:PP:SB 0/1:40,48,0:88:99:1668,0,1165,1787,1309,3096:1672,0,1167,1852,1372,3197:18,22,20,28 +20 10018159 . C . . END=10018554 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:68:0,120,1800:0,134,1835 +20 10018555 . G A, 1567.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.627;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,3,12,63,69,102;RAW_MQ=288000.00;ReadPosRankSum=0.463 GT:AD:DP:GQ:PL:PP:SB 0/1:35,45,0:80:99:1596,0,1211,1701,1347,3048:1593,0,1220,1761,1413,3147:20,15,21,24 +20 10018556 . C . . END=10019092 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:70:0,120,1800:0,136,1838 +20 10019093 . A G, 1244.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.452;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.073;PG=4,0,2,65,63,101;RAW_MQ=245641.00;ReadPosRankSum=-0.230 GT:AD:DP:GQ:PL:PP:SB 0/1:33,36,0:69:99:1273,0,1104,1371,1212,2584:1277,0,1106,1436,1275,2685:15,18,19,17 +20 10019094 . C . . END=10020228 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:60:0,120,1800:0,123,1812 +20 10020229 . G A, 1538.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.792;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.104;PG=0,3,12,63,69,102;RAW_MQ=290210.00;ReadPosRankSum=-0.368 GT:AD:DP:GQ:PL:PP:SB 0/1:38,44,0:82:99:1567,0,1130,1682,1263,2944:1564,0,1139,1742,1329,3043:22,16,24,20 +20 10020230 . T . . END=10023688 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:37:0,93,1395:0,111,1499 +20 10023689 . G A, 1852.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.144;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.352;PG=0,0,6,62,66,101;RAW_MQ=285769.00;ReadPosRankSum=0.764 GT:AD:DP:GQ:PL:PP:SB 0/1:29,51,0:80:99:1881,0,946,1968,1099,3067:1881,0,952,2030,1164,3167:16,13,26,25 +20 10023690 . G . . END=10024106 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:57:0,120,1800:0,140,1846 +20 10024107 . C T, 1694.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.770;ClippingRankSum=0.000;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.546;PG=0,64,104,64,131,104;RAW_MQ=303563.00;ReadPosRankSum=0.329 GT:AD:DP:GQ:PL:PP:SB 0/1:38,48,0:86:99:1723,0,1086,1837,1230,3068:1659,0,1126,1837,1297,3108:21,17,28,20 +20 10024108 . G . . END=10024282 GT:DP:GQ:MIN_DP:PL:PP 0/0:90:99:57:0,120,1800:0,139,1845 +20 10024283 . C . . END=10024283 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:64:62:0,0,1777:0,64,1881 +20 10024284 . T . . END=10024287 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:65:0,120,1800:0,184,1904 +20 10024288 . C . . END=10024288 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:2:71:0,0,1411:0,2,1421 +20 10024289 . T . . END=10024293 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:70:0,120,1800:0,184,1904 +20 10024294 . C . . END=10024294 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:9:69:0,0,1358:0,9,1383 +20 10024295 . T . . END=10024298 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:66:0,37,1800:0,101,1904 +20 10024299 . C . . END=10024299 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:17:62:0,0,1430:0,17,1471 +20 10024300 . CTT C,CT,CTTTT, 87.76 . AC=0,1,1,0;AF=0.00,0.500,0.500,0.00;AN=2;BaseQRankSum=2.446;ClippingRankSum=0.000;DP=50;ExcessHet=3.0103;MLEAC=1,0,1,0;MLEAF=0.500,0.00,0.500,0.00;MQRankSum=-0.600;PG=0,72,110,7,82,20,72,147,82,110,63,137,73,137,101;RAW_MQ=134695.00;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL:PP:SB 2/3:3,4,3,8,0:18:8:122,67,400,91,215,231,19,0,1,156,161,279,257,107,347:39,56,428,15,214,168,8,64,0,184,141,334,247,162,365:1,2,11,4 +20 10024303 . T . . END=10024322 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:99:60:0,57,855:0,121,959 +20 10024323 . T . . END=10024323 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:91:56:0,27,1860:0,91,1964 +20 10024324 . G . . END=10024324 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:64:53:0,0,1491:0,64,1595 +20 10024325 . G . . END=10024325 GT:DP:GQ:MIN_DP:PL:PP 0/0:47:97:47:0,33,1611:0,97,1715 +20 10024326 . A . . END=10026356 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:39:0,58,1509:0,122,1613 +20 10026357 . T C, 1166.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.700;ClippingRankSum=0.000;DP=64;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.148;PG=0,3,12,63,69,102;RAW_MQ=218717.00;ReadPosRankSum=-0.549 GT:AD:DP:GQ:PL:PP:SB 0/1:28,35,0:63:99:1195,0,932,1279,1037,2316:1192,0,941,1339,1103,2415:10,18,20,15 +20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:41:0,102,1530:0,123,1634 +20 10026794 . C T, 1084.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.828;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;PG=0,3,12,63,69,102;RAW_MQ=191641.00;ReadPosRankSum=-0.070 GT:AD:DP:GQ:PL:PP:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:1110,0,538,1230,693,1897:7,12,15,18 +20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:52:0,96,1440:0,160,1544 +20 10027234 . A ATTAG, 1320.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.406;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;PG=4,0,2,64,63,100;RAW_MQ=236651.00;ReadPosRankSum=-0.931 GT:AD:DP:GQ:PL:PP:SB 0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:1362,0,1966,1525,2132,3631:18,16,15,20 +20 10027235 . T . . END=10027235 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:64:72:0,0,334:0,64,438 +20 10027236 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:56:0,120,1800:0,135,1836 +20 10027868 . A G, 1739.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-5.793;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;PG=0,3,12,63,69,102;RAW_MQ=314882.00;ReadPosRankSum=1.229 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:1765,0,3210,1961,3406,5339:19,25,26,19 +20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL:PP 0/0:86:99:85:0,120,1800:0,184,1904 +20 10027872 . A G, 1724.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-5.491;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;PG=0,3,12,63,69,102;RAW_MQ=300482.00;ReadPosRankSum=0.173 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:1750,0,3145,1939,3338,5250:16,24,26,19 +20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:55:0,120,1800:0,123,1812 +20 10028867 . A ATG, 1106.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.874;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;PG=0,6,18,10,18,25;RAW_MQ=338841.00;ReadPosRankSum=0.075 GT:AD:DP:GQ:PL:PP:SB 0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:1138,0,928,1246,1046,2295:11,21,18,21 +20 10028868 . T . . END=10028868 GT:DP:GQ:MIN_DP:PL:PP 0/0:92:64:92:0,0,401:0,64,505 +20 10028869 . G . . END=10030187 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:60:0,120,1800:0,116,1797 +20 10030188 . T A, 1372.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.711;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.013;PG=0,3,12,63,69,102;RAW_MQ=288841.00;ReadPosRankSum=-1.072 GT:AD:DP:GQ:PL:PP:SB 0/1:42,39,0:81:99:1401,0,1524,1527,1641,3168:1398,0,1533,1587,1707,3267:24,18,15,24 +20 10030189 . G . . END=10031253 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:41:0,90,1485:0,117,1566 +20 10031254 . A AT, 1463.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.091;ClippingRankSum=0.000;DP=88;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.017;PG=0,3,12,63,69,102;RAW_MQ=313110.00;ReadPosRankSum=0.478 GT:AD:DP:GQ:PL:PP:SB 0/1:38,47,0:85:99:1501,0,1159,1616,1300,2916:1498,0,1168,1676,1366,3015:27,11,25,22 +20 10031255 . T . . END=10031255 GT:DP:GQ:MIN_DP:PL:PP 0/0:88:64:88:0,0,0:0,64,104 +20 10031256 . G . . END=10031341 GT:DP:GQ:MIN_DP:PL:PP 0/0:96:99:87:0,120,1800:0,184,1904 +20 10031342 . G A, 1834.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.833;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;PG=4,0,2,64,64,101;RAW_MQ=332041.00;ReadPosRankSum=-0.263 GT:AD:DP:GQ:PL:PP:SB 0/1:41,52,0:93:99:1863,0,1375,1986,1531,3517:1867,0,1377,2050,1595,3618:22,19,31,21 +20 10031343 . A . . END=10031797 GT:DP:GQ:MIN_DP:PL:PP 0/0:91:99:66:0,120,1800:0,135,1837 +20 10031798 . G A, 4296.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=104;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=43,18,0,85,64,104;RAW_MQ=369410.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,104,0:104:99:4325,313,0,4325,313,4325:4368,331,0,4410,377,4429:0,0,57,47 +20 10031799 . T . . END=10031826 GT:DP:GQ:MIN_DP:PL:PP 0/0:105:99:101:0,120,1800:0,184,1904 +20 10031827 . C T, 2004.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.552;ClippingRankSum=0.000;DP=108;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.945;PG=0,3,12,63,69,102;RAW_MQ=386569.00;ReadPosRankSum=-0.390 GT:AD:DP:GQ:PL:PP:SB 0/1:52,56,0:108:99:2033,0,1798,2189,1966,4155:2030,0,1807,2249,2032,4254:32,20,29,27 +20 10031828 . T . . END=10032093 GT:DP:GQ:MIN_DP:PL:PP 0/0:102:99:83:0,120,1800:0,184,1904 +20 10032094 . G A, 1220.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.488;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,3,12,63,69,102;RAW_MQ=302400.00;ReadPosRankSum=-0.464 GT:AD:DP:GQ:PL:PP:SB 0/1:47,36,0:83:99:1249,0,1497,1390,1605,2995:1246,0,1506,1450,1671,3094:14,33,16,20 +20 10032095 . T . . END=10032412 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:99:64:0,120,1800:0,143,1851 +20 10032413 . T G, 869.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-6.142;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.065;PG=0,3,12,63,69,102;RAW_MQ=233138.00;ReadPosRankSum=-0.751 GT:AD:DP:GQ:PL:PP:SB 0/1:35,31,0:66:99:898,0,1277,1003,1371,2374:895,0,1286,1063,1437,2473:15,20,20,11 +20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:55:0,120,1800:0,123,1812 +20 10032882 . A T, 1202.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.697;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;PG=5,0,1,65,63,101;RAW_MQ=267241.00;ReadPosRankSum=0.579 GT:AD:DP:GQ:PL:PP:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:1236,0,1407,1413,1577,2963:28,11,22,14 +20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:61:0,90,1350:0,133,1454 +20 10032972 . C CAT, 1122.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.354;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;PG=5,0,1,65,63,101;RAW_MQ=231241.00;ReadPosRankSum=-1.239 GT:AD:DP:GQ:PL:PP:SB 0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:1165,0,1478,1325,1631,2928:17,16,11,19 +20 10032973 . T . . END=10032973 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:64:65:0,0,104:0,64,208 +20 10032974 . G . . END=10034305 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:99:50:0,97,1800:0,137,1839 +20 10034306 . T C, 782.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.661;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.150;PG=0,3,12,63,69,102;RAW_MQ=272210.00;ReadPosRankSum=0.280 GT:AD:DP:GQ:PL:PP:SB 0/1:46,29,0:75:99:811,0,1593,950,1680,2630:808,0,1602,1010,1746,2729:24,22,14,15 +20 10034307 . T . . END=10036106 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:55:0,120,1800:0,117,1801 +20 10036107 . T . . END=10036107 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:65:67:0,1,1807:0,65,1911 +20 10036108 . C . . END=10036140 GT:DP:GQ:MIN_DP:PL:PP 0/0:53:99:41:0,102,1504:0,166,1608 +20 10036141 . C . . END=10036141 GT:DP:GQ:MIN_DP:PL:PP 0/0:46:96:46:0,32,1246:0,96,1350 +20 10036142 . T . . END=10036929 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:99:40:0,81,1385:0,130,1489 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1036.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.200;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;PG=0,0,7,62,66,101;RAW_MQ=274847.00;ReadPosRankSum=0.200 GT:AD:DP:GQ:PL:PP:SB 0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:1074,0,5577,1253,5730,6956:11,28,15,14 +20 10036951 . G . . END=10036951 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:64:77:0,0,1197:0,64,1301 +20 10036952 . A . . END=10036962 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:69:0,37,1800:0,101,1904 +20 10036963 . C . . END=10036963 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:96:72:0,32,2462:0,96,2566 +20 10036964 . C . . END=10037036 GT:DP:GQ:MIN_DP:PL:PP 0/0:86:99:71:0,39,1800:0,103,1844 +20 10037037 . C T, 1436.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.504;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.193;PG=0,2,10,63,68,102;RAW_MQ=293262.00;ReadPosRankSum=-1.694 GT:AD:DP:GQ:PL:PP:SB 0/1:39,42,0:81:99:1465,0,1124,1580,1251,2831:1463,0,1132,1641,1317,2930:28,11,28,14 +20 10037038 . G . . END=10037097 GT:DP:GQ:MIN_DP:PL:PP 0/0:92:99:80:0,111,1665:0,175,1769 +20 10037098 . C . . END=10037098 GT:DP:GQ:MIN_DP:PL:PP 0/0:86:73:86:0,9,2910:0,73,3014 +20 10037099 . A . . END=10037103 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:99:87:0,66,990:0,130,1094 +20 10037104 . T . . END=10037104 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:24:89:0,0,2830:0,24,2883 +20 10037105 . A . . END=10037107 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:99:88:0,54,810:0,118,914 +20 10037108 . G . . END=10037109 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:82:84:0,18,270:0,82,374 +20 10037110 . T TGATA, 2780.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=5,0,1,65,63,101;RAW_MQ=240219.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,61,0:61:99:2818,189,0,2819,190,2820:2822,188,0,2883,252,2920:0,0,35,26 +20 10037111 . G . . END=10037111 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:64:84:0,0,0:0,64,104 +20 10037112 . A . . END=10037121 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:81:0,120,1800:0,184,1904 +20 10037122 . A . . END=10037122 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:21:80:0,0,2281:0,21,2328 +20 10037123 . G . . END=10037124 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:64:80:0,0,2367:0,64,2471 +20 10037125 . T . . END=10037125 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:21:81:0,0,2422:0,21,2469 +20 10037126 . G . . END=10037126 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:64:79:0,0,1989:0,64,2093 +20 10037127 . A . . END=10037131 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:74:0,85,1710:0,149,1814 +20 10037132 . T . . END=10037132 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:21:74:0,0,2013:0,21,2060 +20 10037133 . A . . END=10037134 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:64:72:0,0,1990:0,64,2094 +20 10037135 . A . . END=10037140 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:68:0,93,1395:0,157,1499 +20 10037141 . A . . END=10037143 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:64:68:0,0,1786:0,64,1890 +20 10037144 . T TGATAGATA, 1823.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,3,13,0,7,7;RAW_MQ=187352.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,36,0:36:99:1861,127,0,1864,129,1866:1848,118,0,1852,123,1860:0,0,15,21 +20 10037145 . G . . END=10037145 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:64:75:0,0,8:0,64,112 +20 10037146 . A . . END=10037186 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:65:0,117,1755:0,181,1859 +20 10037187 . G . . END=10037187 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:64:68:0,0,2259:0,64,2363 +20 10037188 . A . . END=10037708 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:49:0,50,1800:0,114,1826 +20 10037709 . A T, 1003.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.367;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.934;PG=0,3,12,63,69,102;RAW_MQ=260041.00;ReadPosRankSum=0.600 GT:AD:DP:GQ:PL:PP:SB 0/1:39,32,0:71:99:1032,0,1354,1150,1450,2600:1029,0,1363,1210,1516,2699:24,15,19,13 +20 10037710 . A . . END=10039370 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:54:0,91,1800:0,103,1809 +20 10039371 . T G, 1324.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.260;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,3,12,63,69,102;RAW_MQ=266400.00;ReadPosRankSum=0.510 GT:AD:DP:GQ:PL:PP:SB 0/1:34,40,0:74:99:1353,0,1194,1455,1315,2770:1350,0,1203,1515,1381,2869:15,19,24,16 +20 10039372 . T . . END=10040754 GT:DP:GQ:MIN_DP:PL:PP 0/0:76:99:56:0,81,1215:0,123,1319 +20 10040755 . G . . END=10040755 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:87:89:0,69,1035:0,87,1077 +20 10040756 . T . . END=10040760 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:99:89:0,45,675:0,109,779 +20 10040761 . C . . END=10040761 GT:DP:GQ:MIN_DP:PL:PP 0/0:88:77:88:0,48,720:0,77,783 +20 10040762 . T . . END=10040762 GT:DP:GQ:MIN_DP:PL:PP 0/0:87:99:87:0,42,630:0,106,734 +20 10040763 . T . . END=10040763 GT:DP:GQ:MIN_DP:PL:PP 0/0:87:94:87:0,30,450:0,94,554 +20 10040764 . T . . END=10040767 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:99:83:0,36,540:0,100,644 +20 10040768 . T . . END=10040771 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:79:81:0,15,225:0,79,329 +20 10040772 . C CT, 1995.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,3,13,11,18,28;RAW_MQ=211048.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,70,0:70:99:2033,210,0,2034,210,2034:2020,201,0,2032,215,2049:0,0,37,33 +20 10040773 . T . . END=10040773 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:64:81:0,0,0:0,64,104 +20 10040774 . T . . END=10040809 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:77:0,42,630:0,106,734 +20 10040810 . C . . END=10040810 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:79:81:0,15,225:0,79,329 +20 10040811 . A . . END=10040811 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:67:80:0,3,45:0,67,149 +20 10040812 . AT A, 2607.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,1,8,29,33,63;RAW_MQ=203299.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,71,0:71:99:2645,214,0,2645,214,2645:2637,207,0,2667,240,2701:0,0,36,35 +20 10040814 . T . . END=10040814 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:64:82:0,0,0:0,64,104 +20 10040815 . T . . END=10040820 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:77:0,75,1800:0,139,1904 +20 10040821 . T A, 1171.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.021;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.097;PG=0,6,18,63,72,103;RAW_MQ=199699.00;ReadPosRankSum=-1.410 GT:AD:DP:GQ:PL:PP:SB 0/1:38,40,0:78:99:1200,0,1099,1314,1219,2533:1194,0,1111,1372,1285,2630:20,18,21,19 +20 10040822 . A . . END=10041303 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:54:0,119,1800:0,135,1835 +20 10041304 . C T, 2765.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=70;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=3,0,3,64,64,101;RAW_MQ=247010.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,68,0:68:99:2794,204,0,2794,204,2794:2795,201,0,2856,265,2892:0,0,34,34 +20 10041305 . G . . END=10041696 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:99:48:0,45,675:0,109,779 +20 10041697 . A . . END=10041697 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:76:75:0,12,180:0,76,284 +20 10041698 . C CAT, 0.04 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.887;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.844;PG=0,8,22,64,74,103;RAW_MQ=265497.00;ReadPosRankSum=0.923 GT:AD:DP:GQ:PL:PP:SB 0/1:48,6,0:54:9:17,0,1425,166,1446,1612:9,0,1439,222,1513,1708:21,27,2,4 +20 10041699 . A . . END=10041699 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:69:77:0,5,2671:0,69,2775 +20 10041700 . T . . END=10041700 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:91:77:0,27,405:0,91,509 +20 10041701 . A ATG,ATATG, 1403.73 . AC=0,1,0;AF=0.00,0.500,0.00;AN=2;BaseQRankSum=0.848;ClippingRankSum=0.000;DP=78;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.340;PG=0,71,108,0,74,6,4,78,7,14;RAW_MQ=270590.00;ReadPosRankSum=0.328 GT:AD:DP:GQ:PL:PP:SB 0/2:8,0,48,0:56:64:1441,1582,2726,0,261,58,1575,2317,264,2201:1441,1653,2834,0,335,64,1579,2395,271,2215:2,6,21,27 +20 10041702 . T . . END=10041702 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:64:75:0,0,0:0,64,104 +20 10041703 . G . . END=10042318 GT:DP:GQ:MIN_DP:PL:PP 0/0:64:99:49:0,117,1800:0,117,1801 +20 10042319 . C T, 2658.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=10,2,0,23,18,43;RAW_MQ=229851.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,66,0:66:99:2687,199,0,2687,199,2687:2697,201,0,2710,217,2730:0,0,38,28 +20 10042320 . C . . END=10042760 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:99:60:0,120,1800:0,135,1836 +20 10042761 . A G, 3553.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=91;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,2,10,63,68,102;RAW_MQ=327600.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,91,0:91:99:3582,272,0,3582,272,3582:3572,264,0,3635,330,3674:0,0,58,33 +20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL:PP 0/0:91:99:79:0,120,1800:0,148,1861 +20 10042829 . A G, 3055.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=78;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=11,2,0,68,63,102;RAW_MQ=278569.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,78,0:78:99:3084,235,0,3084,235,3084:3095,237,0,3152,298,3186:0,0,42,36 +20 10042830 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:56:0,120,1800:0,147,1859 +20 10043002 . A T, 1287.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.986;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,20,46,64,87,104;RAW_MQ=313200.00;ReadPosRankSum=0.178 GT:AD:DP:GQ:PL:PP:SB 0/1:48,38,0:86:99:1316,0,1659,1460,1773,3233:1296,0,1685,1504,1840,3317:19,29,18,20 +20 10043003 . C . . END=10044848 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:44:0,104,1655:0,123,1759 +20 10044849 . A G, 2091.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=60;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,3,11,63,69,102;RAW_MQ=213241.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,59,0:59:99:2120,177,0,2120,177,2120:2109,168,0,2172,234,2211:0,0,22,37 +20 10044850 . C . . END=10045077 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:99:56:0,120,1800:0,129,1824 +20 10045078 . G T, 3271.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=2,0,4,63,65,101;RAW_MQ=279389.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,81,0:81:99:3300,244,0,3300,244,3300:3298,240,0,3359,304,3397:0,0,37,44 +20 10045079 . C . . END=10045641 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:60:0,120,1800:0,129,1825 +20 10045642 . G C, 3107.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,1,7,62,66,101;RAW_MQ=286610.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,81,0:81:99:3136,243,0,3136,243,3136:3129,236,0,3191,302,3230:0,0,38,43 +20 10045643 . A . . END=10046172 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:58:0,39,585:0,103,689 +20 10046173 . A . . END=10046176 GT:DP:GQ:MIN_DP:PL:PP 0/0:63:85:62:0,21,315:0,85,419 +20 10046177 . A . . END=10046177 GT:DP:GQ:MIN_DP:PL:PP 0/0:60:79:60:0,15,225:0,79,329 +20 10046178 . AAGAAAGAAAG A, 2159.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=15,4,0,71,63,103;RAW_MQ=144145.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,50,0:50:99:2197,152,0,2197,152,2197:2212,156,0,2268,215,2300:0,0,23,27 +20 10046189 . A . . END=10046189 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:64:55:0,0,0:0,64,104 +20 10046190 . G . . END=10046536 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:31:0,54,1251:0,110,1355 +20 10046537 . A G, 819.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.909;ClippingRankSum=0.000;DP=57;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.395;PG=9,2,0,67,63,101;RAW_MQ=169333.00;ReadPosRankSum=0.412 GT:AD:DP:GQ:PL:PP:SB 0/1:28,29,0:57:99:848,0,902,932,988,1920:856,0,900,998,1049,2020:13,15,10,19 +20 10046538 . T . . END=10050160 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:43:0,92,1614:0,114,1684 +20 10050161 . A . . END=10050161 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:86:68:0,75,2271:0,86,2299 +20 10050162 . C . . END=10050827 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:52:0,120,1800:0,119,1805 +20 10050828 . T C, 1227.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.704;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.892;PG=1,0,5,63,65,101;RAW_MQ=310441.00;ReadPosRankSum=0.073 GT:AD:DP:GQ:PL:PP:SB 0/1:49,37,0:86:99:1256,0,1768,1403,1879,3282:1257,0,1773,1466,1944,3383:28,21,18,19 +20 10050829 . T . . END=10051447 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:40:0,99,1485:0,126,1589 +20 10051448 . T C, 1134.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.501;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.404;PG=1,0,5,63,65,101;RAW_MQ=247851.00;ReadPosRankSum=-0.549 GT:AD:DP:GQ:PL:PP:SB 0/1:35,35,0:70:99:1163,0,1150,1268,1255,2522:1164,0,1155,1331,1320,2623:27,8,23,12 +20 10051449 . T . . END=10052687 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:55:0,114,1800:0,121,1807 +20 10052688 . C A, 1062.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.180;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.870;PG=0,16,38,64,83,104;RAW_MQ=274969.00;ReadPosRankSum=1.559 GT:AD:DP:GQ:PL:PP:SB 0/1:45,32,0:77:99:1091,0,1645,1226,1741,2967:1075,0,1667,1274,1808,3055:27,18,16,16 +20 10052689 . A . . END=10058021 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:99:36:0,99,1485:0,111,1589 +20 10058022 . T C, 975.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.346;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.466;PG=0,3,13,63,69,102;RAW_MQ=237579.00;ReadPosRankSum=-0.453 GT:AD:DP:GQ:PL:PP:SB 0/1:36,32,0:68:99:1004,0,1261,1112,1357,2469:1001,0,1270,1172,1423,2568:16,20,13,19 +20 10058023 . A . . END=10062934 GT:DP:GQ:MIN_DP:PL:PP 0/0:76:99:46:0,78,1170:0,103,1274 +20 10062935 . CAAA C,CA,CAA,CAAAA, 92.84 . AC=0,0,0,1,0;AF=0.00,0.00,0.00,0.500,0.00;AN=2;BaseQRankSum=1.336;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;MLEAC=0,0,0,1,0;MLEAF=0.00,0.00,0.00,0.500,0.00;MQRankSum=-1.405;PG=0,73,113,73,149,113,73,149,149,113,73,149,149,149,113,64,140,140,140,140,104;RAW_MQ=232368.00;ReadPosRankSum=-0.493 GT:AD:DP:GQ:PL:PP:SB 0/4:5,2,2,4,10,0:23:57:130,219,1823,163,1171,1044,115,628,576,505,0,158,82,16,101,243,986,887,608,171,888:57,219,1863,163,1247,1084,115,704,652,545,0,234,158,92,141,234,1053,954,675,238,919:2,3,9,9 +20 10062939 . A . . END=10065778 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:42:0,76,1575:0,112,1679 +20 10065779 . G . . END=10065779 GT:DP:GQ:MIN_DP:PL:PP 0/0:52:3:52:0,0,1215:0,3,1228 +20 10065780 . T . . END=10067048 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:48:0,38,990:0,102,1094 +20 10067049 . TAAAAAAAAA T,TA,TAA, 613.73 . AC=0,1,1,0;AF=0.00,0.500,0.500,0.00;AN=2;BaseQRankSum=0.177;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.342;PG=0,4,13,4,10,13,71,78,78,110,62,69,69,137,101;RAW_MQ=204256.00;ReadPosRankSum=-0.496 GT:AD:DP:GQ:PL:PP:SB 2/3:2,4,7,9,0:22:90:651,365,925,164,381,340,135,101,0,106,443,591,394,170,627:573,291,860,90,313,275,128,101,0,138,427,582,385,229,650:1,1,12,8 +20 10067059 . A . . END=10067066 GT:DP:GQ:MIN_DP:PL:PP 0/0:59:99:56:0,87,1305:0,151,1409 +20 10067067 . A . . END=10067067 GT:DP:GQ:MIN_DP:PL:PP 0/0:52:83:52:0,19,1692:0,83,1796 +20 10067068 . A . . END=10067068 GT:DP:GQ:MIN_DP:PL:PP 0/0:47:64:47:0,0,1430:0,64,1534 +20 10067069 . A . . END=10067069 GT:DP:GQ:MIN_DP:PL:PP 0/0:42:90:42:0,26,1402:0,90,1506 +20 10067070 . A . . END=10067089 GT:DP:GQ:MIN_DP:PL:PP 0/0:46:99:39:0,84,1471:0,148,1575 +20 10067090 . C A, 2004.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=56;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=4,0,2,65,63,101;RAW_MQ=166789.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,55,0:55:99:2033,164,0,2033,164,2033:2035,162,0,2096,226,2132:0,0,27,28 +20 10067091 . T . . END=10067263 GT:DP:GQ:MIN_DP:PL:PP 0/0:76:99:50:0,120,1800:0,125,1816 +20 10067264 . G A, 2922.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=73;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=1,0,5,63,65,101;RAW_MQ=257282.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,73,0:73:99:2951,219,0,2951,219,2951:2946,214,0,3008,279,3046:0,0,38,35 +20 10067265 . C . . END=10067721 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:52:0,117,1800:0,124,1813 +20 10067722 . A C, 2146.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=55;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=4,0,2,64,64,101;RAW_MQ=198000.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,54,0:54:99:2175,163,0,2175,163,2175:2177,161,0,2237,224,2274:0,0,25,29 +20 10067723 . C . . END=10068157 GT:DP:GQ:MIN_DP:PL:PP 0/0:47:99:27:0,51,765:0,115,869 +20 10068158 . GTGTATATATATA G, 66.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.652;ClippingRankSum=0.000;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.328;PG=0,73,113,64,140,104;RAW_MQ=93364.00;ReadPosRankSum=-0.253 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:3,4,0:7:31:0|1:10068158_GTGTATATATATA_G:104,0,57,114,69,183:31,0,97,105,136,214:0,3,2,2 +20 10068160 . GTATATATATATGTA G, 7.57 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-0.566;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.712;PG=0,73,113,64,140,104;RAW_MQ=87005.00;ReadPosRankSum=0.967 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/0:5,2,0:7:29:1|0:10068158_GTGTATATATATA_G:44,0,134,60,141,201:0,29,203,80,237,261:2,3,0,2 +20 10068175 . T . . END=10068180 GT:DP:GQ:MIN_DP:PL:PP 0/0:19:81:17:0,17,360:0,81,464 +20 10068181 . T . . END=10068185 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:91:16:0,27,405:0,91,509 +20 10068186 . A . . END=10068186 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:73:16:0,9,570:0,73,674 +20 10068187 . T . . END=10068190 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:91:15:0,27,405:0,91,509 +20 10068191 . T . . END=10068193 GT:DP:GQ:MIN_DP:PL:PP 0/0:11:64:11:0,0,289:0,64,393 +20 10068194 . A . . END=10068196 GT:DP:GQ:MIN_DP:PL:PP 0/0:10:91:10:0,27,405:0,91,509 +20 10068197 . T . . END=10068980 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:99:12:0,36,476:0,100,580 +20 10068981 . G A, 2503.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=4,0,2,64,64,101;RAW_MQ=223200.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,61,0:61:99:2532,184,0,2532,184,2532:2533,182,0,2594,245,2631:0,0,27,34 +20 10068982 . A . . END=10070601 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:99:46:0,120,1800:0,121,1809 +20 10070602 . T C, 2691.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=74;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,11,27,64,77,104;RAW_MQ=255364.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,72,0:72:99:2720,216,0,2720,216,2720:2693,199,0,2757,266,2797:0,0,37,35 +20 10070603 . A . . END=10070923 GT:DP:GQ:MIN_DP:PL:PP 0/0:90:99:66:0,57,855:0,121,959 +20 10070924 . T . . END=10070924 GT:DP:GQ:MIN_DP:PL:PP 0/0:89:82:89:0,18,270:0,82,374 +20 10070925 . C . . END=10070926 GT:DP:GQ:MIN_DP:PL:PP 0/0:87:76:86:0,12,180:0,76,284 +20 10070927 . C . . END=10070935 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:64:83:0,0,0:0,64,104 +20 10070936 . T A, 3631.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=81;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,2,11,63,68,102;RAW_MQ=279633.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,81,0:81:99:0|1:10070936_T_A:3660,247,0,3660,247,3660:3649,239,0,3712,305,3751:0,0,44,37 +20 10070937 . A . . END=10070937 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:67:84:0,3,45:0,67,149 +20 10070938 . G GA, 3656.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,2,11,63,68,102;RAW_MQ=275964.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,79,0:79:99:0|1:10070936_T_A:3694,250,0,3694,250,3694:3683,242,0,3746,308,3785:0,0,43,36 +20 10070939 . A . . END=10070939 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:64:83:0,0,0:0,64,104 +20 10070940 . G . . END=10071134 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:67:0,120,1800:0,144,1853 +20 10071135 . C T, 3257.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=14,4,0,70,63,103;RAW_MQ=276123.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,79,0:79:99:3286,238,0,3286,238,3286:3300,242,0,3356,301,3389:0,0,34,45 +20 10071136 . T . . END=10071186 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:78:0,120,1800:0,184,1904 +20 10071187 . G A, 3410.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=82;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,3,12,63,69,102;RAW_MQ=292441.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,82,0:82:99:3439,246,0,3439,246,3439:3427,237,0,3490,303,3529:0,0,30,52 +20 10071188 . G . . END=10071889 GT:DP:GQ:MIN_DP:PL:PP 0/0:61:99:44:0,111,1710:0,123,1813 +20 10071890 . T C, 1974.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=57;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,3,12,63,69,102;RAW_MQ=202969.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,57,0:57:99:2003,171,0,2003,171,2003:1991,162,0,2054,228,2093:0,0,28,29 +20 10071891 . G . . END=10072504 GT:DP:GQ:MIN_DP:PL:PP 0/0:65:99:51:0,120,1800:0,124,1813 +20 10072505 . A G, 2099.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=64;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,11,27,64,77,104;RAW_MQ=230400.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,64,0:64:99:2128,191,0,2128,191,2128:2101,174,0,2164,241,2204:0,0,34,30 +20 10072506 . C . . END=10074186 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:99:40:0,102,1530:0,118,1634 +20 10074187 . A G, 3101.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=79;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,5,16,63,71,103;RAW_MQ=276123.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,79,0:79:99:3130,238,0,3130,238,3130:3114,227,0,3177,293,3217:0,0,36,43 +20 10074188 . T . . END=10074239 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:71:0,120,1800:0,124,1814 +20 10074240 . T C, 3406.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=86;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=13,3,0,69,63,102;RAW_MQ=307369.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,85,0:85:99:3435,255,0,3435,255,3435:3448,258,0,3504,318,3537:0,0,47,38 +20 10074241 . A . . END=10074715 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:41:0,96,1440:0,119,1544 +20 10074716 . G A, 2400.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=66;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=1,0,5,63,65,101;RAW_MQ=232082.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,64,0:64:99:2429,192,0,2429,192,2429:2426,187,0,2487,252,2525:0,0,25,39 +20 10074717 . C . . END=10074805 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:66:0,120,1800:0,133,1832 +20 10074806 . G A, 2817.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=71;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,3,13,63,69,102;RAW_MQ=250077.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,71,0:71:99:2846,213,0,2846,213,2846:2833,204,0,2896,270,2936:0,0,33,38 +20 10074807 . C . . END=10075042 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:56:0,120,1800:0,132,1830 +20 10075043 . T C, 2405.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=62;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=14,4,0,70,63,102;RAW_MQ=220441.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,61,0:61:99:2434,184,0,2434,184,2434:2448,188,0,2504,247,2536:0,0,36,25 +20 10075044 . C . . END=10075141 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:99:51:0,120,1800:0,139,1845 +20 10075142 . G A, 0 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-2.480;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.359;PG=0,64,104,64,131,104;RAW_MQ=222959.00;ReadPosRankSum=-2.348 GT:AD:DP:GQ:PL:PP:SB 0/0:61,4,0:65:99:0,92,2165,183,2177,2268:0,156,2269,247,2308,2372:36,25,0,4 +20 10075143 . A . . END=10075167 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:68:0,120,1800:0,184,1904 +20 10075168 . C T, 3612.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=88;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=0,2,10,63,68,102;RAW_MQ=309981.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,88,0:88:99:3641,264,0,3641,264,3641:3631,256,0,3694,322,3733:0,0,38,50 +20 10075169 . G . . END=10075498 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:49:0,42,630:0,106,734 +20 10075499 . G . . END=10075500 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:91:73:0,27,405:0,91,509 +20 10075501 . T . . END=10075502 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:85:71:0,21,315:0,85,419 +20 10075503 . A . . END=10075506 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:67:72:0,3,45:0,67,149 +20 10075507 . A . . END=10075507 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:70:80:0,6,90:0,70,194 +20 10075508 . GA G, 1928.73 . AC=2,0;AF=1.00,0.00;AN=2;DP=77;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=1,0,5,10,12,25;RAW_MQ=288121.00 GT:AD:DP:GQ:PL:PP:SB 1/1:0,70,0:70:99:1966,210,0,1966,210,1966:1963,205,0,1972,217,1987:0,0,29,41 +20 10075510 . A . . END=10075510 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:64:80:0,0,0:0,64,104 +20 10075511 . A . . END=10076249 GT:DP:GQ:MIN_DP:PL:PP 0/0:76:99:55:0,120,1800:0,119,1804 +20 10076250 . A G, 1107.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.386;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.423;PG=9,1,0,67,63,101;RAW_MQ=282266.00;ReadPosRankSum=-0.605 GT:AD:DP:GQ:PL:PP:SB 0/1:40,39,0:79:99:1136,0,1339,1257,1456,2712:1143,0,1338,1323,1517,2812:14,26,20,19 +20 10076251 . A . . END=10076338 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:62:0,120,1800:0,184,1904 +20 10076339 . A G, 1309.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.069;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.866;PG=8,1,0,67,63,101;RAW_MQ=256441.00;ReadPosRankSum=0.508 GT:AD:DP:GQ:PL:PP:SB 0/1:32,40,0:72:99:1338,0,1035,1435,1156,2590:1345,0,1034,1501,1218,2690:12,20,18,22 +20 10076340 . A . . END=10076398 GT:DP:GQ:MIN_DP:PL:PP 0/0:88:99:72:0,120,1800:0,136,1837 +20 10076399 . G A, 1807.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=4.154;ClippingRankSum=0.000;DP=94;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=7,1,0,66,62,101;RAW_MQ=338400.00;ReadPosRankSum=-0.863 GT:AD:DP:GQ:PL:PP:SB 0/1:44,50,0:94:99:1836,0,1544,1969,1694,3663:1843,0,1543,2034,1756,3763:22,22,22,28 +20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:51:0,102,1530:0,116,1622 +20 10076989 . CAA C,CA,CAAA, 214.73 . AC=0,1,0,0;AF=0.00,0.500,0.00,0.00;AN=2;BaseQRankSum=-0.650;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.463;PG=0,71,110,71,146,110,71,146,146,110,1,75,75,75,8;RAW_MQ=257046.00;ReadPosRankSum=-0.196 GT:AD:DP:GQ:PL:PP:SB 0/2:7,4,13,7,0:31:34:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:140,230,1143,0,482,373,106,310,34,358,210,675,386,281,600:4,3,12,12 +20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:61:0,113,1800:0,177,1904 +20 10077008 . T A, 0 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-1.806;ClippingRankSum=0.000;DP=52;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;PG=0,64,104,64,131,104;RAW_MQ=176164.00;ReadPosRankSum=-2.060 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/0:46,4,0:50:99:0|1:10077008_T_A:0,42,2066,148,2078,2184:0,106,2170,212,2209,2288:18,28,4,0 +20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:99:54:0,120,1800:0,184,1904 +20 10077010 . G A, 0 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-1.841;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;PG=0,64,104,64,131,104;RAW_MQ=183364.00;ReadPosRankSum=-1.996 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/0:48,4,0:52:99:0|1:10077008_T_A:0,42,2066,148,2078,2184:0,106,2170,212,2209,2288:18,30,4,0 +20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:99:44:0,102,1654:0,116,1758 +20 10077752 . T C, 1345.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-6.503;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,12,31,64,79,104;RAW_MQ=284400.00;ReadPosRankSum=-0.142 GT:AD:DP:GQ:PL:PP:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:1362,0,1205,1528,1389,2890:16,18,16,29 +20 10077753 . G . . END=10079475 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:46:0,108,1620:0,116,1724 +20 10079476 . T G, 11.12 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-4.458;ClippingRankSum=0.000;DP=44;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.826;PG=0,16,38,64,83,104;RAW_MQ=153410.00;ReadPosRankSum=-4.313 GT:AD:DP:GQ:PL:PP:SB 0/1:33,11,0:44:23:39,0,1137,137,1166,1304:23,0,1159,185,1233,1392:6,27,11,0 +20 10079477 . A . . END=10081749 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:40:0,84,1485:0,116,1589 +20 10081750 . C A, 1353.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.670;ClippingRankSum=0.000;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,1,8,62,66,101;RAW_MQ=298800.00;ReadPosRankSum=-0.626 GT:AD:DP:GQ:PL:PP:SB 0/1:44,39,0:83:99:1382,0,1525,1514,1643,3157:1381,0,1532,1576,1708,3257:23,21,19,20 +20 10081751 . T . . END=10081799 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:68:0,120,1800:0,184,1904 +20 10081800 . C T, 1109.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.241;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,0,7,62,66,101;RAW_MQ=244800.00;ReadPosRankSum=-1.082 GT:AD:DP:GQ:PL:PP:SB 0/1:35,33,0:68:99:1138,0,1222,1244,1322,2565:1138,0,1229,1306,1387,2665:26,9,17,16 +20 10081801 . A . . END=10082884 GT:DP:GQ:MIN_DP:PL:PP 0/0:76:99:43:0,111,1665:0,121,1769 +20 10082885 . A C, 0 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-2.266;ClippingRankSum=0.000;DP=43;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;PG=0,64,104,64,131,104;RAW_MQ=154800.00;ReadPosRankSum=-2.350 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/0:41,2,0:43:99:0|1:10082885_A_C:0,93,1525,123,1531,1561:0,157,1629,187,1662,1665:18,23,0,2 +20 10082886 . C . . END=10082891 GT:DP:GQ:MIN_DP:PL:PP 0/0:43:99:42:0,99,1485:0,163,1589 +20 10082892 . C T, 1712.77 . AC=2,0;AF=1.00,0.00;AN=2;DP=44;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;PG=8,1,0,67,63,101;RAW_MQ=155641.00 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 1/1:0,44,0:44:99:0|1:10082885_A_C:1741,132,0,1741,132,1741:1749,133,0,1808,195,1842:0,0,20,24 +20 10082893 . C . . END=10085210 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:35:0,75,1220:0,117,1324 +20 10085211 . A T, 1210.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.501;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.028;PG=0,3,12,63,69,102;RAW_MQ=272210.00;ReadPosRankSum=-0.280 GT:AD:DP:GQ:PL:PP:SB 0/1:40,36,0:76:99:1239,0,1443,1360,1551,2911:1236,0,1452,1420,1617,3010:21,19,17,19 +20 10085212 . G . . END=10086109 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:54:0,120,1800:0,117,1800 +20 10086110 . G A, 1274.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.343;ClippingRankSum=0.000;DP=81;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.680;PG=9,2,0,67,63,101;RAW_MQ=283323.00;ReadPosRankSum=0.875 GT:AD:DP:GQ:PL:PP:SB 0/1:43,38,0:81:99:1303,0,1506,1432,1621,3053:1311,0,1504,1498,1682,3153:24,19,19,19 +20 10086111 . C . . END=10086282 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:99:55:0,120,1800:0,184,1904 +20 10086283 . G T, 1025.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.304;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=9,2,0,67,63,101;RAW_MQ=306000.00;ReadPosRankSum=1.608 GT:AD:DP:GQ:PL:PP:SB 0/1:52,32,0:84:99:1054,0,1771,1210,1867,3077:1062,0,1769,1276,1928,3177:30,22,17,15 +20 10086284 . G . . END=10086618 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:51:0,120,1800:0,140,1845 +20 10086619 . T A, 796.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.256;ClippingRankSum=0.000;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.312;PG=0,6,17,63,72,103;RAW_MQ=250610.00;ReadPosRankSum=-0.051 GT:AD:DP:GQ:PL:PP:SB 0/1:45,25,0:70:99:825,0,1603,961,1679,2639:819,0,1615,1019,1745,2736:18,27,9,16 +20 10086620 . T . . END=10086852 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:65:0,120,1800:0,124,1814 +20 10086853 . G A, 1002.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.915;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.177;PG=10,2,0,68,63,102;RAW_MQ=257810.00;ReadPosRankSum=-0.270 GT:AD:DP:GQ:PL:PP:SB 0/1:41,32,0:73:99:1031,0,1280,1154,1376,2530:1039,0,1278,1220,1437,2630:21,20,17,15 +20 10086854 . T . . END=10086953 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:60:0,120,1800:0,184,1904 +20 10086954 . G A, 1095.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.606;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=10,2,0,68,63,102;RAW_MQ=244800.00;ReadPosRankSum=-0.812 GT:AD:DP:GQ:PL:PP:SB 0/1:34,34,0:68:99:1124,0,1051,1226,1153,2380:1132,0,1049,1292,1214,2480:16,18,21,13 +20 10086955 . C . . END=10087229 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:55:0,120,1800:0,146,1858 +20 10087230 . A G, 1842.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.407;ClippingRankSum=0.000;DP=96;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.707;PG=10,2,0,68,63,102;RAW_MQ=332861.00;ReadPosRankSum=0.893 GT:AD:DP:GQ:PL:PP:SB 0/1:42,54,0:96:99:1871,0,1428,1998,1590,3588:1879,0,1426,2064,1651,3688:22,20,23,31 +20 10087231 . C . . END=10087393 GT:DP:GQ:MIN_DP:PL:PP 0/0:101:99:84:0,120,1800:0,145,1855 +20 10087394 . T G, 1688.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.340;ClippingRankSum=0.000;DP=84;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.207;PG=0,6,17,63,72,103;RAW_MQ=299641.00;ReadPosRankSum=1.181 GT:AD:DP:GQ:PL:PP:SB 0/1:35,49,0:84:99:1717,0,1186,1823,1334,3156:1711,0,1198,1881,1400,3253:21,14,24,25 +20 10087395 . T . . END=10087753 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:61:0,120,1800:0,129,1823 +20 10087754 . T G, 1347.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.355;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.193;PG=0,3,12,63,69,102;RAW_MQ=288141.00;ReadPosRankSum=-0.831 GT:AD:DP:GQ:PL:PP:SB 0/1:37,41,0:78:99:1376,0,1239,1488,1362,2849:1373,0,1248,1548,1428,2948:23,14,24,17 +20 10087755 . G . . END=10087803 GT:DP:GQ:MIN_DP:PL:PP 0/0:102:99:83:0,120,1800:0,141,1849 +20 10087804 . C T, 1619.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.940;ClippingRankSum=0.000;DP=100;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.618;PG=10,2,0,68,63,102;RAW_MQ=369310.00;ReadPosRankSum=1.024 GT:AD:DP:GQ:PL:PP:SB 0/1:50,50,0:100:99:1648,0,1511,1797,1661,3458:1656,0,1509,1863,1722,3558:33,17,28,22 +20 10087805 . G . . END=10087819 GT:DP:GQ:MIN_DP:PL:PP 0/0:101:99:97:0,120,1800:0,184,1904 +20 10087820 . CAG C,CAGAG, 428.73 . AC=0,1,0;AF=0.00,0.500,0.00;AN=2;BaseQRankSum=-1.974;ClippingRankSum=0.000;DP=99;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=0.422;PG=3,72,109,5,78,13,0,72,5,3;RAW_MQ=362700.00;ReadPosRankSum=-0.009 GT:AD:DP:GQ:PL:PP:SB 0/2:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:464,736,2681,0,1269,1176,656,2304,1238,2187:17,18,8,10 +20 10087823 . A . . END=10088062 GT:DP:GQ:MIN_DP:PL:PP 0/0:94:99:71:0,64,1800:0,128,1854 +20 10088063 . C T, 1417.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.405;ClippingRankSum=0.000;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.515;PG=10,2,0,68,63,102;RAW_MQ=327579.00;ReadPosRankSum=0.354 GT:AD:DP:GQ:PL:PP:SB 0/1:49,44,0:93:99:1446,0,1403,1592,1535,3128:1454,0,1401,1658,1596,3228:24,25,18,26 +20 10088064 . G . . END=10088698 GT:DP:GQ:MIN_DP:PL:PP 0/0:87:99:60:0,120,1800:0,141,1848 +20 10088699 . C T, 776.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.803;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.140;PG=10,2,0,68,63,102;RAW_MQ=199738.00;ReadPosRankSum=-0.577 GT:AD:DP:GQ:PL:PP:SB 0/1:36,26,0:62:99:805,0,1088,913,1166,2079:813,0,1086,979,1227,2179:15,21,19,7 +20 10088700 . G . . END=10088729 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:99:52:0,120,1800:0,184,1904 +20 10088730 . G A, 972.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.224;ClippingRankSum=0.000;DP=53;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.839;PG=10,2,0,68,63,102;RAW_MQ=149199.00;ReadPosRankSum=0.433 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:29,23,0:52:99:0|1:10088730_G_A:1001,0,1152,1092,1231,2322:1009,0,1150,1158,1292,2422:11,18,16,7 +20 10088731 . G . . END=10088735 GT:DP:GQ:MIN_DP:PL:PP 0/0:56:99:56:0,120,1800:0,184,1904 +20 10088736 . A C, 1081.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.282;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.169;PG=10,2,0,68,63,102;RAW_MQ=150523.00;ReadPosRankSum=-0.042 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:28,27,0:55:99:0|1:10088730_G_A:1110,0,1194,1203,1281,2484:1118,0,1192,1269,1342,2584:10,18,16,11 +20 10088737 . C . . END=10088746 GT:DP:GQ:MIN_DP:PL:PP 0/0:57:99:53:0,120,1800:0,184,1904 +20 10088747 . A G, 1111.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-3.877;ClippingRankSum=0.000;DP=56;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.907;PG=9,1,0,67,63,101;RAW_MQ=147080.00;ReadPosRankSum=-0.339 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:1147,0,994,1285,1146,2404:10,15,18,11 +20 10088748 . G . . END=10088798 GT:DP:GQ:MIN_DP:PL:PP 0/0:50:99:46:0,109,1710:0,173,1814 +20 10088799 . G A, 1018.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.503;ClippingRankSum=0.000;DP=54;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.498;PG=11,3,0,69,63,102;RAW_MQ=150881.00;ReadPosRankSum=1.347 GT:AD:DP:GQ:PL:PP:SB 0/1:22,31,0:53:99:1047,0,617,1114,711,1824:1056,0,614,1180,771,1923:14,8,12,19 +20 10088800 . T . . END=10088842 GT:DP:GQ:MIN_DP:PL:PP 0/0:54:99:36:0,63,945:0,127,1049 +20 10088843 . C . . END=10088843 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:80:25:0,16,759:0,80,863 +20 10088844 . A . . END=10088894 GT:DP:GQ:MIN_DP:PL:PP 0/0:32:99:25:0,37,718:0,101,822 +20 10088895 . C T, 532.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.462;ClippingRankSum=0.000;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;PG=8,1,0,67,63,101;RAW_MQ=135291.00;ReadPosRankSum=0.907 GT:AD:DP:GQ:PL:PP:SB 0/1:23,18,0:41:99:561,0,673,630,726,1356:568,0,672,696,787,1456:10,13,8,10 +20 10088896 . G . . END=10088965 GT:DP:GQ:MIN_DP:PL:PP 0/0:50:99:42:0,55,1485:0,119,1589 +20 10088966 . C . . END=10088967 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:64:70:0,0,2081:0,64,2185 +20 10088968 . C CAAA, 1175.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.497;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;PG=5,0,1,8,6,17;RAW_MQ=177808.00;ReadPosRankSum=1.015 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:1218,0,1368,1318,1469,2790:16,14,14,9 +20 10088969 . A . . END=10088969 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:64:72:0,0,1374:0,64,1478 +20 10088970 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:75:0,57,1800:0,121,1904 +20 10088980 . T C, 1247.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.585;ClippingRankSum=0.000;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;PG=10,2,0,68,63,102;RAW_MQ=176353.00;ReadPosRankSum=0.999 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:1284,0,1625,1460,1790,3223:19,18,15,16 +20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:77:0,40,1800:0,104,1904 +20 10088985 . T C, 1178.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.192;ClippingRankSum=0.000;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;PG=10,2,0,68,63,102;RAW_MQ=191764.00;ReadPosRankSum=1.381 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:1215,0,1727,1399,1887,3259:22,20,15,17 +20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:81:0,120,1800:0,184,1904 +20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:71:84:0,7,2771:0,71,2875 +20 10088991 . C . . END=10089025 GT:DP:GQ:MIN_DP:PL:PP 0/0:84:99:76:0,88,1800:0,152,1904 +20 10089026 . G . . END=10089026 GT:DP:GQ:MIN_DP:PL:PP 0/0:74:11:74:0,0,2116:0,11,2143 +20 10089027 . A . . END=10089036 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:76:0,83,1800:0,147,1904 +20 10089037 . G . . END=10089037 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:50:82:0,40,2255:0,50,2281 +20 10089038 . A . . END=10089440 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:74:0,79,1800:0,117,1800 +20 10089441 . A G, 1179.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-4.885;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.948;PG=0,2,11,63,68,102;RAW_MQ=270841.00;ReadPosRankSum=0.161 GT:AD:DP:GQ:PL:PP:SB 0/1:37,39,0:76:99:1208,0,1313,1319,1430,2749:1206,0,1322,1379,1496,2848:19,18,14,25 +20 10089442 . G . . END=10089524 GT:DP:GQ:MIN_DP:PL:PP 0/0:82:99:74:0,120,1800:0,184,1904 +20 10089525 . C T, 1548.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.859;ClippingRankSum=0.000;DP=82;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.531;PG=10,2,0,68,63,102;RAW_MQ=290210.00;ReadPosRankSum=0.428 GT:AD:DP:GQ:PL:PP:SB 0/1:38,43,0:81:99:1577,0,1088,1691,1217,2908:1585,0,1086,1757,1278,3008:22,16,20,23 +20 10089526 . G . . END=10090288 GT:DP:GQ:MIN_DP:PL:PP 0/0:72:99:55:0,78,1170:0,126,1274 +20 10090289 . CAA C,CA, 384.73 . AC=0,1,0;AF=0.00,0.500,0.00;AN=2;BaseQRankSum=0.441;ClippingRankSum=0.000;DP=80;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.393;PG=5,0,1,3,2,8,64,62,65,99;RAW_MQ=287682.00;ReadPosRankSum=-0.223 GT:AD:DP:GQ:PL:PP:SB 0/2:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:423,357,984,0,259,235,537,926,410,1023:7,7,11,13 +20 10090292 . A . . END=10090763 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:99:61:0,38,1800:0,102,1837 +20 10090764 . A G, 840.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.659;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=16,5,0,71,63,103;RAW_MQ=226800.00;ReadPosRankSum=0.695 GT:AD:DP:GQ:PL:PP:SB 0/1:34,29,0:63:99:869,0,1207,972,1294,2265:880,0,1202,1038,1352,2363:12,22,14,15 +20 10090765 . A . . END=10090969 GT:DP:GQ:MIN_DP:PL:PP 0/0:75:99:65:0,120,1800:0,117,1800 +20 10090970 . T C, 1257.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.484;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.509;PG=0,1,8,63,67,101;RAW_MQ=247538.00;ReadPosRankSum=0.429 GT:AD:DP:GQ:PL:PP:SB 0/1:33,36,0:69:99:1286,0,1092,1384,1201,2585:1285,0,1099,1446,1267,2685:20,13,20,16 +20 10090971 . C . . END=10091213 GT:DP:GQ:MIN_DP:PL:PP 0/0:61:99:49:0,120,1800:0,126,1819 +20 10091214 . C T, 1249.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.361;ClippingRankSum=0.000;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;PG=0,3,12,63,69,102;RAW_MQ=249769.00;ReadPosRankSum=0.392 GT:AD:DP:GQ:PL:PP:SB 0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:1275,0,1119,1437,1288,2698:11,22,13,24 +20 10091215 . C . . END=10092414 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:99:46:0,120,1800:0,116,1798 +20 10092415 . A G, 1635.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-6.731;ClippingRankSum=0.000;DP=102;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,3,12,63,69,102;RAW_MQ=367200.00;ReadPosRankSum=-0.070 GT:AD:DP:GQ:PL:PP:SB 0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:1661,0,1911,1880,2115,3969:27,25,24,25 +20 10092416 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL:PP 0/0:80:99:60:0,120,1800:0,117,1801 +20 10092927 . G T, 106.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.507;ClippingRankSum=0.000;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;PG=0,12,30,64,79,104;RAW_MQ=257282.00;ReadPosRankSum=-4.416 GT:AD:DP:GQ:PL:PP:SB 0/1:59,13,0:72:99:135,0,1864,310,1901,2211:123,0,1882,362,1968,2303:43,16,0,13 +20 10092928 . T . . END=10093567 GT:DP:GQ:MIN_DP:PL:PP 0/0:79:99:57:0,75,1125:0,128,1229 +20 10093568 . GTT G,GT,GTTT, 326.73 . AC=0,1,0,0;AF=0.00,0.500,0.00,0.00;AN=2;BaseQRankSum=0.426;ClippingRankSum=0.000;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,0;MLEAF=0.00,0.500,0.00,0.00;MQRankSum=0.410;PG=3,72,108,2,74,8,72,144,74,108,0,72,2,72,3;RAW_MQ=203561.00;ReadPosRankSum=0.987 GT:AD:DP:GQ:PL:PP:SB 0/2:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:365,399,1228,0,502,391,447,852,365,1015,429,908,449,850,886:7,10,10,15 +20 10093571 . T . . END=10093922 GT:DP:GQ:MIN_DP:PL:PP 0/0:62:99:51:0,59,1485:0,123,1589 +20 10093923 . T A, 1075.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.667;ClippingRankSum=0.000;DP=67;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.358;PG=0,3,12,63,69,102;RAW_MQ=234704.00;ReadPosRankSum=-2.256 GT:AD:DP:GQ:PL:PP:SB 0/1:35,32,0:67:99:1104,0,1257,1209,1353,2563:1101,0,1266,1269,1419,2662:18,17,15,17 +20 10093924 . G . . END=10094250 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:99:53:0,120,1800:0,136,1838 +20 10094251 . T A, 1270.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.251;ClippingRankSum=0.000;DP=63;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;PG=0,3,12,63,69,102;RAW_MQ=226800.00;ReadPosRankSum=1.734 GT:AD:DP:GQ:PL:PP:SB 0/1:26,36,0:62:99:1299,0,781,1376,889,2265:1296,0,790,1436,955,2364:10,16,23,13 +20 10094252 . C . . END=10094581 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:46:0,117,1755:0,129,1824 +20 10094582 . A G, 923.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.388;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.270;PG=0,20,46,64,87,104;RAW_MQ=254210.00;ReadPosRankSum=-0.527 GT:AD:DP:GQ:PL:PP:SB 0/1:39,30,0:69:99:952,0,1350,1070,1440,2510:932,0,1376,1114,1507,2594:20,19,16,14 +20 10094583 . T . . END=10094773 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:67:0,120,1800:0,135,1835 +20 10094774 . C T, 1036.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.784;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;PG=0,3,12,63,69,102;RAW_MQ=274441.00;ReadPosRankSum=0.494 GT:AD:DP:GQ:PL:PP:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:1062,0,1291,1245,1451,2669:24,16,21,14 +20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:63:0,120,1800:0,126,1818 +20 10095432 . GTGATGATGA G, 839.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.265;ClippingRankSum=0.000;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;PG=6,3,7,0,0,0;RAW_MQ=227748.00;ReadPosRankSum=0.660 GT:AD:DP:GQ:PL:PP:SB 0/1:27,23,0:50:99:877,0,2108,959,2181,3140:880,0,2111,956,2178,3137:16,11,12,11 +20 10095442 . T . . END=10095442 GT:DP:GQ:MIN_DP:PL:PP 0/0:71:64:71:0,0,1080:0,64,1184 +20 10095443 . G . . END=10095740 GT:DP:GQ:MIN_DP:PL:PP 0/0:81:99:64:0,120,1800:0,130,1826 +20 10095741 . A G, 1075.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.534;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;PG=0,1,8,63,67,101;RAW_MQ=237128.00;ReadPosRankSum=-0.326 GT:AD:DP:GQ:PL:PP:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:1103,0,1240,1275,1401,2647:14,22,18,16 +20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL:PP 0/0:73:99:63:0,120,1800:0,130,1826 +20 10096293 . C T, 1355.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=4.664;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.397;PG=0,3,11,63,69,102;RAW_MQ=260861.00;ReadPosRankSum=0.012 GT:AD:DP:GQ:PL:PP:SB 0/1:37,38,0:75:99:1384,0,1258,1495,1372,2867:1381,0,1267,1555,1438,2966:21,16,21,17 +20 10096294 . T . . END=10096595 GT:DP:GQ:MIN_DP:PL:PP 0/0:68:99:57:0,120,1800:0,117,1801 +20 10096596 . C T, 1562.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.728;ClippingRankSum=0.000;DP=87;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.612;PG=0,2,9,63,67,101;RAW_MQ=300461.00;ReadPosRankSum=0.166 GT:AD:DP:GQ:PL:PP:SB 0/1:40,47,0:87:99:1591,0,1273,1711,1414,3125:1589,0,1281,1772,1480,3225:19,21,23,24 +20 10096597 . T . . END=10096767 GT:DP:GQ:MIN_DP:PL:PP 0/0:90:99:75:0,120,1800:0,115,1796 +20 10096768 . A C, 1682.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.764;ClippingRankSum=0.000;DP=91;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.609;PG=12,3,0,69,63,102;RAW_MQ=319323.00;ReadPosRankSum=0.541 GT:AD:DP:GQ:PL:PP:SB 0/1:42,49,0:91:99:1711,0,1452,1838,1600,3437:1720,0,1449,1904,1660,3536:25,17,24,25 +20 10096769 . A . . END=10096898 GT:DP:GQ:MIN_DP:PL:PP 0/0:78:99:65:0,99,1485:0,136,1589 +20 10096899 . G T, 1614.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.755;ClippingRankSum=0.000;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.387;PG=13,3,0,70,63,102;RAW_MQ=279938.00;ReadPosRankSum=0.378 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:1652,0,1517,1830,1709,3512:19,20,12,28 +20 10096900 . G . . END=10096904 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:99:79:0,108,1620:0,172,1724 +20 10096905 . TA T, 1600.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.755;ClippingRankSum=0.000;DP=83;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.677;PG=13,3,0,70,63,102;RAW_MQ=291579.00;ReadPosRankSum=0.397 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:1647,0,1620,1834,1812,3619:20,20,13,30 +20 10096907 . A . . END=10096907 GT:DP:GQ:MIN_DP:PL:PP 0/0:83:64:83:0,0,0:0,64,104 +20 10096908 . T . . END=10096932 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:99:83:0,120,1800:0,132,1831 +20 10096933 . G C, 1511.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.914;ClippingRankSum=0.000;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.802;PG=13,3,0,70,63,102;RAW_MQ=298779.00;ReadPosRankSum=0.238 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:1549,0,1767,1750,1956,3679:28,16,13,28 +20 10096934 . T . . END=10096957 GT:DP:GQ:MIN_DP:PL:PP 0/0:91:99:87:0,120,1800:0,184,1904 +20 10096958 . G A, 1766.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.839;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.701;PG=15,4,0,71,63,103;RAW_MQ=323979.00;ReadPosRankSum=-1.860 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:1805,0,1625,1995,1832,3800:27,18,16,31 +20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL:PP 0/0:92:99:84:0,120,1800:0,184,1904 +20 10097075 . T G, 1445.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.533;ClippingRankSum=0.000;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;PG=12,3,0,69,63,102;RAW_MQ=315628.00;ReadPosRankSum=-0.285 GT:AD:DP:GQ:PL:PP:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:1483,0,1479,1672,1686,3331:18,26,26,22 +20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL:PP 0/0:92:99:79:0,99,1485:0,163,1589 +20 10097101 . C CTTT,CTTTT, 1091.73 . AC=1,0,0;AF=0.500,0.00,0.00;AN=2;BaseQRankSum=-1.134;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;PG=5,4,8,0,2,1,64,65,62,99;RAW_MQ=252294.00;ReadPosRankSum=1.111 GT:AD:DP:GQ:PL:PP:SB 0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:1130,0,1311,554,1322,2009,1042,1492,2110,2472:22,12,15,15 +20 10097102 . T . . END=10097102 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:64:77:0,0,200:0,64,304 +20 10097103 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL:PP 0/0:70:99:60:0,99,1485:0,133,1589 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1054.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.820;ClippingRankSum=0.000;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;PG=0,73,113,64,140,104;RAW_MQ=262143.00;ReadPosRankSum=-3.231 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:57,32,0:89:99:0|1:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:1092,0,2241,1263,2338,3601:1019,0,2281,1254,2405,3632:23,34,11,21 +20 10097437 . TTTTC T, 796.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.791;ClippingRankSum=0.000;DP=76;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=4.881;PG=14,16,24,4,9,0;RAW_MQ=217330.00;ReadPosRankSum=2.929 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:32,23,0:55:99:1|0:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:834,0,1193,931,1263,2194:832,0,1201,919,1256,2178:11,21,5,18 +20 10097442 . T . . END=10097442 GT:DP:GQ:MIN_DP:PL:PP 0/0:63:64:63:0,0,698:0,64,802 +20 10097443 . T . . END=10097455 GT:DP:GQ:MIN_DP:PL:PP 0/0:63:99:61:0,71,1125:0,135,1229 +20 10097456 . T . . END=10097458 GT:DP:GQ:MIN_DP:PL:PP 0/0:64:64:61:0,0,1556:0,64,1660 +20 10097459 . T . . END=10097460 GT:DP:GQ:MIN_DP:PL:PP 0/0:61:85:60:0,21,2071:0,85,2175 +20 10097461 . C . . END=10097475 GT:DP:GQ:MIN_DP:PL:PP 0/0:61:64:58:0,0,1102:0,64,1206 +20 10097476 . T . . END=10097476 GT:DP:GQ:MIN_DP:PL:PP 0/0:66:75:66:0,11,2255:0,75,2359 +20 10097477 . C . . END=10097625 GT:DP:GQ:MIN_DP:PL:PP 0/0:69:99:45:0,109,1710:0,140,1814 +20 10097626 . C A, 626.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.085;ClippingRankSum=0.000;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.331;PG=0,2,11,63,68,102;RAW_MQ=162820.00;ReadPosRankSum=1.154 GT:AD:DP:GQ:PL:PP:SB 0/1:28,20,0:48:99:655,0,957,739,1017,1757:653,0,965,800,1083,1856:8,20,8,12 +20 10097627 . T . . END=10097788 GT:DP:GQ:MIN_DP:PL:PP 0/0:60:99:49:0,120,1800:0,116,1797 +20 10097789 . T C, 688.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.157;ClippingRankSum=0.000;DP=61;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.805;PG=13,3,0,69,63,102;RAW_MQ=204439.00;ReadPosRankSum=-0.092 GT:AD:DP:GQ:PL:PP:SB 0/1:34,23,0:57:99:717,0,1190,820,1260,2079:726,0,1187,886,1320,2178:14,20,13,10 +20 10097790 . C . . END=10097927 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:37:0,88,1395:0,107,1430 +20 10097928 . G A, 570.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.203;ClippingRankSum=0.000;DP=40;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.654;PG=13,3,0,69,63,102;RAW_MQ=135723.00;ReadPosRankSum=0.057 GT:AD:DP:GQ:PL:PP:SB 0/1:17,19,0:36:99:599,0,586,650,643,1293:609,0,583,716,703,1392:9,8,8,11 +20 10097929 . A . . END=10098109 GT:DP:GQ:MIN_DP:PL:PP 0/0:37:99:33:0,84,1260:0,112,1361 +20 10098110 . G C, 586.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.510;ClippingRankSum=0.000;DP=36;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.477;PG=13,4,0,70,63,102;RAW_MQ=124082.00;ReadPosRankSum=-0.714 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:19,17,0:36:99:0|1:10098110_G_C:615,0,727,672,779,1451:625,0,723,738,838,1549:0,19,2,15 +20 10098111 . T . . END=10098134 GT:DP:GQ:MIN_DP:PL:PP 0/0:35:99:34:0,84,1260:0,118,1364 +20 10098135 . C A, 471.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.155;ClippingRankSum=0.000;DP=38;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.546;PG=13,4,0,70,63,102;RAW_MQ=135182.00;ReadPosRankSum=-0.769 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:24,14,0:38:99:0|1:10098110_G_C:500,0,964,575,1006,1581:510,0,960,641,1065,1680:0,24,1,13 +20 10098136 . A . . END=10098214 GT:DP:GQ:MIN_DP:PL:PP 0/0:31:99:24:0,36,540:0,100,644 +20 10098215 . T . . END=10098217 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:91:21:0,27,405:0,91,509 +20 10098218 . G . . END=10098218 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:86:21:0,22,768:0,86,872 +20 10098219 . TATATATA T, 295.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.147;ClippingRankSum=0.000;DP=21;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.205;PG=12,3,0,69,63,102;RAW_MQ=65705.00;ReadPosRankSum=0.498 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:12,9,0:21:99:0|1:10098219_TATATATA_T:333,0,461,369,488,858:342,0,458,435,548,957:0,12,0,9 +20 10098227 . T . . END=10098227 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:64:18:0,0,86:0,64,190 +20 10098228 . T . . END=10098228 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:78:18:0,14,662:0,78,766 +20 10098229 . A . . END=10098231 GT:DP:GQ:MIN_DP:PL:PP 0/0:18:80:18:0,16,315:0,80,419 +20 10098232 . T . . END=10098232 GT:DP:GQ:MIN_DP:PL:PP 0/0:17:75:17:0,11,615:0,75,719 +20 10098233 . A . . END=10098235 GT:DP:GQ:MIN_DP:PL:PP 0/0:16:85:14:0,21,315:0,85,419 +20 10098236 . T . . END=10098236 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:27:12:0,21,315:0,27,333 +20 10098237 . A T, 244.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.006;ClippingRankSum=0.000;DP=13;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.742;PG=1,0,5,63,65,100;RAW_MQ=37064.00;ReadPosRankSum=0.277 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:6,7,0:13:99:0|1:10098219_TATATATA_T:273,0,273,294,294,588:274,0,278,357,359,688:0,6,0,7 +20 10098238 . A . . END=10098238 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:85:12:0,21,315:0,85,419 +20 10098239 . T . . END=10098239 GT:DP:GQ:MIN_DP:PL:PP 0/0:12:27:12:0,21,315:0,27,333 +20 10098240 . A . . END=10098255 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:82:8:0,18,270:0,82,374 +20 10098256 . T . . END=10098264 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:73:6:0,9,135:0,73,239 +20 10098265 . T C, 133.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.834;ClippingRankSum=0.000;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.834;PG=0,64,104,64,131,104;RAW_MQ=10564.00;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:2,4,0:6:98:0|1:10098219_TATATATA_T:162,0,59,168,71,239:98,0,99,168,138,279:0,2,0,4 +20 10098266 . A . . END=10098307 GT:DP:GQ:MIN_DP:PL:PP 0/0:3:70:2:0,6,86:0,70,190 +20 10098308 . AAT A, 0 . AC=0,0;AF=0.00,0.00;AN=2;DP=2;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;PG=0,73,113,64,140,104;RAW_MQ=7200.00 GT:AD:DP:GQ:PL:PP:SB 0/0:2,0,0:2:70:0,6,81,6,81,81:0,79,194,70,221,185:0,2,0,0 +20 10098311 . A . . END=10098343 GT:DP:GQ:MIN_DP:PL:PP 0/0:3:70:2:0,6,80:0,70,184 +20 10098344 . A . . END=10098344 GT:DP:GQ:MIN_DP:PL:PP 0/0:4:64:4:0,0,1:0,64,105 +20 10098345 . T . . END=10098357 GT:DP:GQ:MIN_DP:PL:PP 0/0:3:70:3:0,6,90:0,70,194 +20 10098358 . T . . END=10098491 GT:DP:GQ:MIN_DP:PL:PP 0/0:1:64:0:0,0,0:0,64,104 +20 10098492 . A . . . GT:AD:DP:GQ:PL:PP 1/1:0,0:0:15:0,0,0:35,15,0 +20 10098493 . A . . END=10098599 GT:DP:GQ:MIN_DP:PL:PP 0/0:0:64:0:0,0,0:0,64,104 +20 10098600 . G . . END=10098600 GT:DP:GQ:MIN_DP:PL:PP 0/0:1:5:1:0,3,43:0,5,52 +20 10098601 . T . . END=10098672 GT:DP:GQ:MIN_DP:PL:PP 0/0:1:64:1:0,0,0:0,64,104 +20 10098673 . A . . END=10098696 GT:DP:GQ:MIN_DP:PL:PP 0/0:3:70:2:0,6,72:0,70,176 +20 10098697 . A . . END=10098712 GT:DP:GQ:MIN_DP:PL:PP 0/0:6:82:6:0,18,231:0,82,335 +20 10098713 . A . . END=10098713 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:64:8:0,0,262:0,64,366 +20 10098714 . T . . END=10098722 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:88:8:0,24,297:0,88,401 +20 10098723 . T . . END=10098723 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:74:8:0,10,265:0,74,369 +20 10098724 . G . . END=10098724 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:22:8:0,24,297:0,22,300 +20 10098725 . T . . END=10098732 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:85:7:0,21,289:0,85,393 +20 10098733 . T . . END=10098733 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:73:9:0,9,309:0,73,413 +20 10098734 . A . . END=10098738 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:88:8:0,24,310:0,88,414 +20 10098739 . T . . END=10098740 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:91:9:0,27,353:0,91,457 +20 10098741 . A . . END=10098749 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:88:9:0,24,360:0,88,464 +20 10098750 . A . . END=10098750 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:64:9:0,0,289:0,64,393 +20 10098751 . T . . END=10098756 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:88:8:0,24,298:0,88,402 +20 10098757 . T . . END=10098761 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:91:9:0,27,343:0,91,447 +20 10098762 . A . . END=10098762 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:88:9:0,24,360:0,88,464 +20 10098763 . T . . END=10098770 GT:DP:GQ:MIN_DP:PL:PP 0/0:10:91:10:0,27,405:0,91,509 +20 10098771 . A . . END=10098782 GT:DP:GQ:MIN_DP:PL:PP 0/0:10:82:10:0,18,270:0,82,374 +20 10098783 . A . . END=10098783 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:79:9:0,15,225:0,79,329 +20 10098784 . T . . END=10098785 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:82:9:0,18,270:0,82,374 +20 10098786 . C . . END=10098786 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:64:9:0,0,168:0,64,272 +20 10098787 . A . . END=10098787 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:82:9:0,18,270:0,82,374 +20 10098788 . C . . END=10098788 GT:DP:GQ:MIN_DP:PL:PP 0/0:8:79:8:0,15,225:0,79,329 +20 10098789 . T . . END=10098800 GT:DP:GQ:MIN_DP:PL:PP 0/0:9:82:8:0,18,270:0,82,374 +20 10098801 . T . . END=10098809 GT:DP:GQ:MIN_DP:PL:PP 0/0:10:91:9:0,27,326:0,91,430 +20 10098810 . G . . END=10098858 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:99:14:0,36,540:0,100,644 +20 10098859 . G . . END=10098859 GT:DP:GQ:MIN_DP:PL:PP 0/0:24:93:24:0,29,851:0,93,955 +20 10098860 . T . . END=10098867 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:99:23:0,57,855:0,121,959 +20 10098868 . C . . END=10098868 GT:DP:GQ:MIN_DP:PL:PP 0/0:25:74:25:0,54,810:0,74,856 +20 10098869 . G . . END=10098884 GT:DP:GQ:MIN_DP:PL:PP 0/0:30:99:27:0,45,675:0,109,779 +20 10098885 . C CA, 433.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=0.165;ClippingRankSum=0.000;DP=31;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.449;PG=11,2,0,68,62,101;RAW_MQ=77157.00;ReadPosRankSum=-0.159 GT:AD:DP:GQ:PL:PP:SB 0/1:17,14,0:31:99:471,0,572,523,614,1137:479,0,570,588,674,1236:16,1,13,1 +20 10098886 . C . . END=10098886 GT:DP:GQ:MIN_DP:PL:PP 0/0:31:64:31:0,0,240:0,64,344 +20 10098887 . C . . END=10098910 GT:DP:GQ:MIN_DP:PL:PP 0/0:30:99:28:0,66,990:0,104,1094 +20 10098911 . G . . END=10098911 GT:DP:GQ:MIN_DP:PL:PP 0/0:27:82:27:0,63,945:0,82,988 +20 10098912 . C . . END=10098920 GT:DP:GQ:MIN_DP:PL:PP 0/0:26:99:23:0,54,810:0,118,914 +20 10098921 . C . . END=10098921 GT:DP:GQ:MIN_DP:PL:PP 0/0:23:67:23:0,54,810:0,67,842 +20 10098922 . C . . END=10098944 GT:DP:GQ:MIN_DP:PL:PP 0/0:21:99:19:0,45,675:0,109,779 +20 10098945 . T C, 452.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.475;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.504;PG=11,2,0,67,62,100;RAW_MQ=57553.00;ReadPosRankSum=0.837 GT:AD:DP:GQ:PL:PP:SB 0/1:9,13,0:22:99:481,0,248,508,288,795:489,0,246,573,348,893:8,1,13,0 +20 10098946 . C . . END=10098986 GT:DP:GQ:MIN_DP:PL:PP 0/0:24:99:22:0,55,842:0,119,946 +20 10098987 . C T, 379.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.127;ClippingRankSum=0.000;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.734;PG=0,7,20,63,73,102;RAW_MQ=64586.00;ReadPosRankSum=0.348 GT:AD:DP:GQ:PL:PP:SB 0/1:11,13,0:24:99:408,0,350,441,389,830:401,0,363,497,455,925:9,2,13,0 +20 10098988 . G . . END=10099028 GT:DP:GQ:MIN_DP:PL:PP 0/0:24:99:22:0,60,890:0,124,994 +20 10099029 . T C, 334.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.809;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;PG=13,3,0,70,63,102;RAW_MQ=79617.00;ReadPosRankSum=-0.793 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:373,0,765,486,858,1317:14,4,9,1 +20 10099030 . C . . END=10099033 GT:DP:GQ:MIN_DP:PL:PP 0/0:28:99:28:0,63,945:0,127,1049 +20 10099034 . C A, 334.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=2.757;ClippingRankSum=0.000;DP=28;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.641;PG=13,3,0,70,63,102;RAW_MQ=79617.00;ReadPosRankSum=-1.540 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:373,0,765,486,858,1317:13,5,9,1 +20 10099035 . G . . END=10099043 GT:DP:GQ:MIN_DP:PL:PP 0/0:28:99:24:0,51,765:0,115,869 +20 10099044 . A C, 334.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.148;ClippingRankSum=0.000;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;PG=13,3,0,70,63,102;RAW_MQ=59851.00;ReadPosRankSum=-2.625 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:373,0,765,486,858,1317:12,3,7,2 +20 10099045 . C . . END=10099045 GT:DP:GQ:MIN_DP:PL:PP 0/0:24:99:24:0,60,900:0,124,1004 +20 10099046 . T C, 304.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-2.165;ClippingRankSum=0.000;DP=24;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.418;PG=13,3,0,70,63,102;RAW_MQ=59851.00;ReadPosRankSum=-2.686 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:343,0,600,444,690,1107:12,3,7,2 +20 10099047 . G . . END=10099051 GT:DP:GQ:MIN_DP:PL:PP 0/0:26:99:25:0,63,945:0,127,1049 +20 10099052 . G . . END=10099052 GT:DP:GQ:MIN_DP:PL:PP 0/0:26:92:26:0,66,990:0,92,1048 +20 10099053 . G . . END=10099054 GT:DP:GQ:MIN_DP:PL:PP 0/0:27:99:26:0,63,945:0,127,1049 +20 10099055 . T C, 256.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.554;ClippingRankSum=0.000;DP=23;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.316;PG=13,3,0,70,63,102;RAW_MQ=58555.00;ReadPosRankSum=-2.131 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:295,0,670,402,757,1132:11,4,6,2 +20 10099056 . T . . END=10099078 GT:DP:GQ:MIN_DP:PL:PP 0/0:31:99:28:0,75,1118:0,139,1222 +20 10099079 . C T, 116.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.434;ClippingRankSum=0.000;DP=29;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.821;PG=13,3,0,70,63,102;RAW_MQ=78698.00;ReadPosRankSum=1.966 GT:AD:DP:GQ:PGT:PID:PL:PP:SB 0/1:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:155,0,883,283,964,1219:11,12,4,2 +20 10099080 . G . . END=10099110 GT:DP:GQ:MIN_DP:PL:PP 0/0:40:99:35:0,66,990:0,99,1094 +20 10099111 . T TTTTGTTTG, 656.73 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.207;ClippingRankSum=0.000;DP=42;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.071;PG=7,0,0,28,25,55;RAW_MQ=109737.00;ReadPosRankSum=-0.120 GT:AD:DP:GQ:PL:PP:SB 0/1:22,13,0:35:99:694,0,802,763,859,1622:700,0,802,791,883,1676:13,9,7,6 +20 10099112 . T . . END=10099112 GT:DP:GQ:MIN_DP:PL:PP 0/0:55:64:55:0,0,194:0,64,298 +20 10099113 . T . . END=10099139 GT:DP:GQ:MIN_DP:PL:PP 0/0:63:99:57:0,120,1800:0,184,1904 +20 10099140 . G T, 1005.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.114;ClippingRankSum=0.000;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.469;PG=12,3,0,69,63,102;RAW_MQ=192512.00;ReadPosRankSum=0.169 GT:AD:DP:GQ:PL:PP:SB 0/1:30,32,0:62:99:1034,0,931,1122,1028,2150:1043,0,928,1188,1088,2249:18,12,22,10 +20 10099141 . G . . END=10099189 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:64:0,120,1800:0,184,1904 +20 10099190 . G T, 1034.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-0.034;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.711;PG=11,3,0,68,63,102;RAW_MQ=220251.00;ReadPosRankSum=-1.418 GT:AD:DP:GQ:PL:PP:SB 0/1:33,32,0:65:99:1063,0,1154,1162,1251,2413:1072,0,1151,1228,1311,2512:21,12,21,11 +20 10099191 . C . . END=10099219 GT:DP:GQ:MIN_DP:PL:PP 0/0:59:99:46:0,111,1665:0,175,1769 +20 10099220 . A G, 577.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.664;ClippingRankSum=0.000;DP=45;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.596;PG=14,4,0,70,63,102;RAW_MQ=149477.00;ReadPosRankSum=0.331 GT:AD:DP:GQ:PL:PP:SB 0/1:25,20,0:45:99:606,0,873,681,933,1614:616,0,869,747,992,1712:15,10,11,9 +20 10099221 . T . . END=10099249 GT:DP:GQ:MIN_DP:PL:PP 0/0:41:99:35:0,84,1260:0,148,1364 +20 10099250 . G A, 699.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=3.170;ClippingRankSum=0.000;DP=37;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.272;PG=0,3,11,63,68,102;RAW_MQ=119006.00;ReadPosRankSum=0.169 GT:AD:DP:GQ:PL:PP:SB 0/1:16,21,0:37:99:728,0,424,776,487,1263:725,0,433,836,553,1362:12,4,11,10 +20 10099251 . A . . END=10099269 GT:DP:GQ:MIN_DP:PL:PP 0/0:30:99:28:0,81,1132:0,145,1236 +20 10099270 . A C, 0 . AC=0,0;AF=0.00,0.00;AN=2;BaseQRankSum=-2.866;ClippingRankSum=0.000;DP=30;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-2.691;PG=0,11,28,64,78,104;RAW_MQ=98268.00;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL:PP:SB 0/0:27,3,0:30:71:0,60,1084,81,1092,1113:0,71,1112,145,1170,1217:19,8,0,3 +20 10099271 . C . . END=10099534 GT:DP:GQ:MIN_DP:PL:PP 0/0:57:99:31:0,84,1260:0,124,1364 +20 10099535 . G A, 1335.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=5.034;ClippingRankSum=0.000;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.418;PG=13,3,0,69,63,102;RAW_MQ=226251.00;ReadPosRankSum=-0.508 GT:AD:DP:GQ:PL:PP:SB 0/1:26,39,0:65:99:1364,0,686,1442,803,2245:1373,0,683,1508,863,2344:17,9,22,17 +20 10099536 . T . . END=10099564 GT:DP:GQ:MIN_DP:PL:PP 0/0:67:99:63:0,120,1800:0,184,1904 +20 10099565 . C T, 1346.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=4.595;ClippingRankSum=0.000;DP=69;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.266;PG=13,3,0,69,63,102;RAW_MQ=243410.00;ReadPosRankSum=0.740 GT:AD:DP:GQ:PL:PP:SB 0/1:31,38,0:69:99:1375,0,994,1468,1108,2576:1384,0,991,1534,1168,2675:23,8,21,17 +20 10099566 . T . . END=10099754 GT:DP:GQ:MIN_DP:PL:PP 0/0:77:99:66:0,120,1800:0,135,1835 +20 10099755 . C T, 1098.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=1.550;ClippingRankSum=0.000;DP=66;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.022;PG=13,3,0,69,63,102;RAW_MQ=232610.00;ReadPosRankSum=-0.684 GT:AD:DP:GQ:PL:PP:SB 0/1:33,32,0:65:99:1127,0,1148,1226,1245,2470:1136,0,1145,1292,1305,2569:20,13,17,15 +20 10099756 . C . . END=10099831 GT:DP:GQ:MIN_DP:PL:PP 0/0:64:99:59:0,120,1800:0,184,1904 +20 10099832 . A G, 1073.77 . AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-4.563;ClippingRankSum=0.000;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.869;PG=16,5,0,71,63,103;RAW_MQ=250276.00;ReadPosRankSum=0.213 GT:AD:DP:GQ:PL:PP:SB 0/1:39,33,0:72:99:1102,0,1430,1220,1530,2749:1113,0,1425,1286,1588,2847:22,17,14,19 +20 10099833 . T . . END=10100000 GT:DP:GQ:MIN_DP:PL:PP 0/0:85:99:73:0,120,1800:0,138,1842 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 new file mode 100644 index 00000000000..ab58c3364a7 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected.posteriors.genotyped.vcf @@ -0,0 +1,289 @@ +##fileformat=VCFv4.2 +##ALT= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GATKCommandLine= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##source=GenotypeGVCFs +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10000117 . C T 905.77 . 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=14.15;ReadPosRankSum=-1.790e-01;SOR=1.538 GT:AD:DP:GQ:PL:PP 0/1:36,28:64:99:934,0,1248:939,0,1249,1107,1395,2475 +20 10000211 . C T 941.77 . 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=17.77;ReadPosRankSum=1.07;SOR=0.944 GT:AD:DP:GQ:PL:PP 0/1:26,27:53:99:970,0,906:975,0,907,1114,1051,2137 +20 10000439 . T G 2804.77 . 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;SOR=1.236 GT:AD:DP:GQ:PL:PP 1/1:0,80:80:99:2833,240,0:2846,243,0,2902,303,2935 +20 10000598 . T A 1941.77 . 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;SOR=1.225 GT:AD:DP:GQ:PL:PP 1/1:0,49:49:99:1970,147,0:1983,150,0,2039,210,2072 +20 10000694 . G A 1008.77 . 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=12.30;ReadPosRankSum=0.182;SOR=0.566 GT:AD:DP:GQ:PL:PP 0/1:45,37:82:99:1037,0,1601:1042,0,1602,1238,1775,2986 +20 10000758 . T A 3838.77 . 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;SOR=0.802 GT:AD:DP:GQ:PL:PP 1/1:0,95:95:99:3867,286,0:3879,289,0,3936,349,3969 +20 10001019 . T G 650.77 . 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=10.01;ReadPosRankSum=-1.497e+00;SOR=0.665 GT:AD:DP:GQ:PL:PP 0/1:39,26:65:99:679,0,1426:682,0,1429,860,1568,2400 +20 10001298 . T A 2917.77 . 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;SOR=0.963 GT:AD:DP:GQ:PL:PP 1/1:0,73:73:99:2946,220,0:2959,223,0,3015,283,3048 +20 10001436 . A AAGGCT 2301.73 . 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;SOR=3.442 GT:AD:DP:GQ:PL:PP 1/1:0,50:50:99:2339,156,0:2350,159,0,2408,220,2442 +20 10001474 . C T 2640.77 . 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;SOR=1.516 GT:AD:DP:GQ:PL:PP 1/1:0,73:73:99:2669,219,0:2681,222,0,2738,282,2771 +20 10001617 . C A 1731.77 . 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=16.81;ReadPosRankSum=-5.780e-01;SOR=1.346 GT:AD:DP:GQ:PL:PP 0/1:52,51:103:99:1760,0,1781:1765,0,1782,1981,1998,3952 +20 10001628 . G A 3898.77 . 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;SOR=1.053 GT:AD:DP:GQ:PL:PP 1/1:0,95:95:99:3927,285,0:3940,288,0,3997,348,4029 +20 10001661 . T C 3606.77 . 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;SOR=1.193 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,81:81:99:1|1:10001661_T_C:3635,249,0:3648,252,0,3704,312,3737 +20 10001670 . T G 3673.77 . 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;SOR=0.995 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,81:81:99:1|1:10001661_T_C:3702,253,0:3715,256,0,3771,316,3804 +20 10002058 . T G 2963.77 . 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;ReadPosRankSum=-5.240e-01;SOR=0.776 GT:AD:DP:GQ:PL:PP 1/1:1,74:75:99:2992,216,0:3005,219,0,3063,286,3103 +20 10002099 . C T 1194.77 . 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=18.38;ReadPosRankSum=-3.600e-01;SOR=0.375 GT:AD:DP:GQ:PL:PP 0/1:27,38:65:99:1223,0,844:1218,0,855,1362,1024,2360 +20 10002138 . C G 2443.77 . 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;SOR=0.730 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,53:53:99:1|1:10002138_C_G:2472,169,0:2484,172,0,2541,232,2574 +20 10002142 . G C 2407.77 . 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;SOR=0.853 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,52:52:99:1|1:10002138_C_G:2436,166,0:2448,169,0,2505,229,2538 +20 10002470 . C T 2522.77 . AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.62;QD=31.98;SOR=0.941 GT:AD:DP:GQ:PL:PP 1/1:0,61:61:99:2551,189,0:2563,192,0,2620,252,2653 +20 10002625 . G T 2665.77 . AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=27.51;SOR=1.127 GT:AD:DP:GQ:PL:PP 1/1:0,64:64:99:2694,193,0:2706,196,0,2763,256,2796 +20 10003021 . C T 2383.77 . AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;QD=29.11;SOR=1.071 GT:AD:DP:GQ:PL:PP 1/1:0,60:60:99:2412,181,0:2425,184,0,2482,244,2514 +20 10003358 . A C 1454.77 . 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=16.35;ReadPosRankSum=-4.440e-01;SOR=0.572 GT:AD:DP:GQ:PL:PP 0/1:45,44:89:99:1483,0,1477:1488,0,1478,1683,1672,3328 +20 10003651 . T C 3620.77 . AC=2;AF=1.00;AN=2;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=28.08;SOR=1.511 GT:AD:DP:GQ:PL:PP 1/1:0,93:93:99:3649,279,0:3662,282,0,3718,342,3751 +20 10003692 . A G 2609.77 . AC=2;AF=1.00;AN=2;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;QD=23.23;SOR=1.352 GT:AD:DP:GQ:PL:PP 1/1:0,68:68:99:2638,205,0:2651,208,0,2707,268,2740 +20 10003832 . G A 2705.77 . AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.13;QD=29.03;SOR=1.473 GT:AD:DP:GQ:PL:PP 1/1:0,66:66:99:2734,199,0:2747,202,0,2803,262,2836 +20 10004094 . A C 1825.77 . AC=2;AF=1.00;AN=2;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.75;QD=34.45;SOR=1.524 GT:AD:DP:GQ:PL:PP 1/1:0,53:53:99:1854,157,0:1867,160,0,1923,220,1956 +20 10004147 . A G 1837.77 . AC=2;AF=1.00;AN=2;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.99;QD=30.67;SOR=1.136 GT:AD:DP:GQ:PL:PP 1/1:0,52:52:99:1866,156,0:1878,159,0,1935,219,1968 +20 10004193 . G T 918.77 . 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=17.67;ReadPosRankSum=0.775;SOR=1.019 GT:AD:DP:GQ:PL:PP 0/1:23,29:52:99:947,0,775:930,0,798,1063,927,1962 +20 10004222 . C CA 12.96 . 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=0.33;ReadPosRankSum=-5.200e-02;SOR=0.434 GT:AD:DP:GQ:PL:PP 0/1:31,8:39:50:50,0,923:0,22,985,115,990,1085 +20 10004223 . A AG 47.73 . 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=1.02;ReadPosRankSum=2.23;SOR=0.638 GT:AD:DP:GQ:PL:PP 0/1:36,11:47:85:85,0,982:72,0,1001,244,1084,1301 +20 10004351 . C G 2755.77 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=26.61;SOR=0.874 GT:AD:DP:GQ:PL:PP 1/1:0,70:70:99:2784,211,0:2797,214,0,2853,274,2886 +20 10004389 . T G 2494.77 . AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;QD=29.20;SOR=1.143 GT:AD:DP:GQ:PL:PP 1/1:0,62:62:99:2523,187,0:2536,190,0,2592,250,2625 +20 10004610 . A C 3625.77 . AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;QD=28.55;SOR=0.761 GT:AD:DP:GQ:PL:PP 1/1:0,89:89:99:3654,267,0:3667,270,0,3723,330,3756 +20 10004725 . A G 951.77 . 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=14.64;ReadPosRankSum=1.79;SOR=0.605 GT:AD:DP:GQ:PL:PP 0/1:35,30:65:99:980,0,1168:978,0,1176,1145,1324,2442 +20 10004769 . TAAAACTATGC T 981.73 . 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=15.34;ReadPosRankSum=2.22;SOR=1.306 GT:AD:DP:GQ:PL:PP 0/1:37,27:64:99:1019,0,1471:1014,0,1482,1189,1620,2782 +20 10004874 . A C 3602.77 . AC=2;AF=1.00;AN=2;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.33;QD=34.42;SOR=1.286 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,87:87:99:1|1:10004874_A_C:3631,261,0:3651,268,0,3705,325,3734 +20 10004887 . A G 1323.77 . 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=15.57;ReadPosRankSum=-1.600e-01;SOR=0.984 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:45,40:85:99:0|1:10004874_A_C:1352,0,1542:1347,0,1553,1545,1728,3247 +20 10005010 . C T 2934.77 . AC=2;AF=1.00;AN=2;DP=72;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=28.53;SOR=1.226 GT:AD:DP:GQ:PL:PP 1/1:0,72:72:99:2963,217,0:2976,220,0,3032,280,3065 +20 10005427 . C T 2214.77 . AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;QD=27.23;SOR=0.729 GT:AD:DP:GQ:PL:PP 1/1:0,55:55:99:2243,165,0:2256,168,0,2313,228,2345 +20 10005499 . A G 3053.77 . AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.52;SOR=1.121 GT:AD:DP:GQ:PL:PP 1/1:0,76:76:99:3082,229,0:3095,232,0,3151,292,3184 +20 10005587 . A G 1229.77 . 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=17.08;ReadPosRankSum=0.649;SOR=0.848 GT:AD:DP:GQ:PL:PP 0/1:36,36:72:99:1258,0,1236:1263,0,1237,1431,1408,2811 +20 10005723 . A G 3062.77 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=33.47;SOR=0.947 GT:AD:DP:GQ:PL:PP 1/1:0,86:86:99:3091,258,0:3104,261,0,3160,321,3193 +20 10006291 . G A 978.77 . 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=11.65;ReadPosRankSum=-1.614e+00;SOR=0.659 GT:AD:DP:GQ:PL:PP 0/1:53,31:84:99:1007,0,1905:1008,0,1910,1230,2063,3266 +20 10006404 . A C 2928.77 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.16;QD=32.91;SOR=1.432 GT:AD:DP:GQ:PL:PP 1/1:0,76:76:99:2957,228,0:2970,231,0,3026,291,3059 +20 10006682 . T A 2874.77 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=31.31;SOR=1.179 GT:AD:DP:GQ:PL:PP 1/1:0,73:73:99:2903,219,0:2916,222,0,2972,282,3005 +20 10006819 . AAAAC A 2531.73 . AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.13;QD=31.45;SOR=0.762 GT:AD:DP:GQ:PL:PP 1/1:0,58:58:99:2569,176,0:2580,179,0,2592,193,2609 +20 10007150 . G C 669.77 . 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=10.63;ReadPosRankSum=-1.745e+00;SOR=0.746 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:38,25:63:99:0|1:10007150_G_C:698,0,1479:693,0,1490,871,1620,2464 +20 10007175 . C T 1350.77 . 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=22.14;ReadPosRankSum=-7.300e-01;SOR=0.434 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:23,38:61:99:1|0:10007150_G_C:1379,0,780:1380,0,785,1511,959,2444 +20 10007352 . C T 2764.77 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=33.27;SOR=1.054 GT:AD:DP:GQ:PL:PP 1/1:0,69:69:99:2793,208,0:2806,211,0,2862,271,2895 +20 10007531 . A G 2920.77 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;QD=31.26;SOR=1.577 GT:AD:DP:GQ:PL:PP 1/1:0,72:72:99:2949,217,0:2962,220,0,3018,280,3051 +20 10007980 . A C 3524.77 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.72;QD=27.76;SOR=0.990 GT:AD:DP:GQ:PL:PP 1/1:0,90:90:99:3553,270,0:3565,273,0,3622,333,3655 +20 10008029 . T TA 1986.73 . 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=26.49;ReadPosRankSum=-1.055e+00;SOR=0.788 GT:AD:DP:GQ:PL:PP 1/1:3,72:75:99:2024,145,0:2033,147,0,2045,229,2131 +20 10008146 . TA T 2141.73 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.59;QD=30.60;SOR=0.874 GT:AD:DP:GQ:PL:PP 1/1:0,70:70:99:2179,211,0:2192,214,0,2248,274,2281 +20 10008221 . T C 3224.77 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=29.09;SOR=0.850 GT:AD:DP:GQ:PL:PP 1/1:0,80:80:99:3253,240,0:3266,243,0,3322,303,3355 +20 10008458 . T G 2654.77 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.54;QD=26.08;SOR=0.980 GT:AD:DP:GQ:PL:PP 1/1:0,69:69:99:2683,207,0:2696,210,0,2752,270,2785 +20 10008742 . G T 715.77 . 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=14.61;ReadPosRankSum=0.772;SOR=0.741 GT:AD:DP:GQ:PL:PP 0/1:23,26:49:99:744,0,580:739,0,591,871,724,1568 +20 10008758 . C CA 684.14 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;ClippingRankSum=0.00;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=2;MLEAF=1.00;MQ=35.24;MQRankSum=-1.168e+00;QD=19.55;ReadPosRankSum=-2.340e-01;SOR=0.249 GT:AD:DP:GQ:PL:PP 1/1:4,31:35:10:721,10,0:721,7,0,741,110,846 +20 10008921 . C CA 253.73 . 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=7.46;ReadPosRankSum=-4.150e-01;SOR=0.512 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:18,16:34:99:0|1:10008921_C_CA:291,0,366:290,0,373,357,431,792 +20 10008948 . TA T 2057.73 . 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=33.85;ReadPosRankSum=0.749;SOR=0.818 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:1,50:51:99:1|1:10008921_C_CA:2095,107,0:2107,110,0,2167,222,2252 +20 10008952 . CACACACACACA C,CCACACACACA 1666.73 . 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=27.08;ReadPosRankSum=0.685;SOR=1.127 GT:AD:DP:GQ:PL:PP 1/2:1,14,11:34:99:1704,525,845,582,0,530:1624,868,1290,450,811,780,718,582,173,735,574,410,0,511,562,1068,1100,685,788,615,1273 +20 10009227 . A G 1369.77 . 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=22.09;ReadPosRankSum=-1.093e+00;SOR=0.281 GT:AD:DP:GQ:PL:PP 0/1:23,39:62:99:1398,0,740:1393,0,751,1526,923,2423 +20 10009246 . A G 3002.77 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=25.42;SOR=0.887 GT:AD:DP:GQ:PL:PP 1/1:0,77:77:99:3031,231,0:3051,238,0,3105,295,3134 +20 10009400 . T A 2998.77 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.65;SOR=0.804 GT:AD:DP:GQ:PL:PP 1/1:0,74:74:99:3027,223,0:3040,226,0,3096,286,3129 +20 10009512 . C G 3039.77 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.47;QD=29.48;SOR=1.223 GT:AD:DP:GQ:PL:PP 1/1:0,77:77:99:3068,231,0:3081,234,0,3137,294,3170 +20 10009719 . A G 1895.77 . AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.29;QD=32.13;SOR=0.950 GT:AD:DP:GQ:PL:PP 1/1:0,59:59:99:1924,175,0:1932,176,0,1991,238,2025 +20 10009795 . A G 1880.77 . AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=30.56;SOR=1.514 GT:AD:DP:GQ:PL:PP 1/1:0,47:47:99:1909,141,0:1921,144,0,1978,204,2011 +20 10009842 . G GAA 532.73 . 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=15.67;ReadPosRankSum=0.052;SOR=0.738 GT:AD:DP:GQ:PL:PP 0/1:19,15:34:99:570,0,690:554,0,712,677,805,1455 +20 10009844 . G A 661.77 . 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=18.91;ReadPosRankSum=0.259;SOR=0.793 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:16,19:35:99:0|1:10009844_G_A:690,0,586:685,0,597,797,710,1479 +20 10009871 . A G 658.77 . 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=18.30;ReadPosRankSum=1.57;SOR=0.553 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:17,19:36:99:0|1:10009844_G_A:687,0,594:683,0,604,798,718,1489 +20 10009875 . A G,AGGGAGG 2378.77 . 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=33.63;ReadPosRankSum=-8.300e-02;SOR=0.599 GT:AD:DP:GQ:PL:PP 1/2:2,15,13:30:99:2407,645,533,697,0,574:2330,570,466,692,0,608,1867,646,761,1830 +20 10009879 . A G 2244.77 . 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=30.55;ReadPosRankSum=1.39;SOR=1.474 GT:AD:DP:GQ:PL:PP 1/1:2,47:49:99:2273,150,0:2270,146,0,2335,214,2375 +20 10009883 . A G 2151.77 . AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.56;QD=32.62;SOR=1.659 GT:AD:DP:GQ:PL:PP 1/1:0,47:47:99:2180,147,0:2187,147,0,2246,209,2282 +20 10010393 . T G 1464.77 . 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=18.54;ReadPosRankSum=-1.630e+00;SOR=0.606 GT:AD:DP:GQ:PL:PP 0/1:36,43:79:99:1493,0,1230:1488,0,1241,1659,1425,3059 +20 10010536 . G GA 2462.73 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.63;QD=31.17;SOR=0.881 GT:AD:DP:GQ:PL:PP 1/1:0,79:79:99:2500,243,0:2513,246,0,2569,307,2602 +20 10010766 . T G 2411.77 . AC=2;AF=1.00;AN=2;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.33;SOR=0.818 GT:AD:DP:GQ:PL:PP 1/1:0,66:66:99:2440,199,0:2453,202,0,2509,262,2542 +20 10010832 . T C 2951.77 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;QD=35.36;SOR=1.091 GT:AD:DP:GQ:PL:PP 1/1:0,75:75:99:2980,226,0:2993,229,0,3049,289,3082 +20 10011075 . C T 1325.77 . 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=15.97;ReadPosRankSum=-1.057e+00;SOR=0.968 GT:AD:DP:GQ:PL:PP 0/1:44,39:83:99:1354,0,1333:1358,0,1335,1550,1513,3036 +20 10011309 . T C 2692.77 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.97;SOR=1.223 GT:AD:DP:GQ:PL:PP 1/1:0,77:77:99:2721,231,0:2734,234,0,2790,294,2823 +20 10011517 . GA G 490.73 . 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=7.55;ReadPosRankSum=1.15;SOR=0.394 GT:AD:DP:GQ:PL:PP 0/1:37,28:73:99:528,0,875:529,624,2151,0,1057,880,623,1533,743,1691,730,1778,1031,1554,1739 +20 10011666 . C T 2961.77 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=34.30;SOR=1.103 GT:AD:DP:GQ:PL:PP 1/1:0,73:73:99:2990,220,0:3003,223,0,3059,283,3092 +20 10011939 . C T 2469.77 . AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.26;QD=27.00;SOR=1.292 GT:AD:DP:GQ:PL:PP 1/1:0,61:61:99:2498,184,0:2511,187,0,2567,247,2600 +20 10012021 . CA C 1975.73 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;QD=29.94;SOR=1.196 GT:AD:DP:GQ:PL:PP 1/1:0,66:66:99:2013,198,0:2026,201,0,2082,261,2115 +20 10012362 . G T 835.77 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.78;QD=30.82;SOR=4.003 GT:AD:DP:GQ:PL:PP 1/1:0,23:23:69:864,69,0:871,70,0,875,76,884 +20 10012384 . T C 229.77 . 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=12.76;ReadPosRankSum=0.190;SOR=0.044 GT:AD:DP:GQ:PL:PP 0/1:10,8:18:99:258,0,355:261,0,358,352,443,768 +20 10012387 . T C 533.77 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.96;QD=33.36;SOR=3.258 GT:AD:DP:GQ:PL:PP 1/1:0,16:16:50:562,50,0:573,52,0,630,113,664 +20 10012479 . A G 592.77 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=34.87;SOR=0.804 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,17:17:50:1|1:10012479_A_G:621,50,0:632,52,0,688,112,721 +20 10012498 . C G 466.77 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.03;QD=29.27;SOR=1.270 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,11:11:33:1|1:10012479_A_G:495,33,0:507,36,0,563,95,595 +20 10012518 . T C 406.77 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.96;QD=35.92;SOR=0.892 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,9:9:30:1|1:10012479_A_G:435,30,0:445,32,0,502,92,535 +20 10012521 . C T 46.77 . 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=4.25;ReadPosRankSum=1.97;SOR=1.179 GT:AD:DP:GQ:PL:PP 0/1:8,3:11:75:75,0,224:79,0,226,162,296,431 +20 10012570 . G GCA 457.73 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.55;QD=29.63;SOR=3.056 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,9:9:33:1|1:10012570_G_GCA:495,33,0:505,35,0,562,95,595 +20 10012572 . GT G 457.73 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.52;QD=28.76;SOR=3.442 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,11:11:33:1|1:10012570_G_GCA:495,33,0:505,35,0,562,95,595 +20 10012631 . C CG 484.73 . 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=23.08;ReadPosRankSum=-8.350e-01;SOR=0.048 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:8,13:21:99:0|1:10012631_C_CG:522,0,297:519,0,306,605,401,980 +20 10012636 . G C 527.77 . 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=23.99;ReadPosRankSum=-7.180e-01;SOR=0.058 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:8,14:22:99:0|1:10012631_C_CG:556,0,294:553,0,303,640,401,1014 +20 10012714 . G C 1300.77 . AC=2;AF=1.00;AN=2;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.04;QD=29.94;SOR=2.964 GT:AD:DP:GQ:PL:PP 1/1:0,35:35:99:1329,105,0:1341,108,0,1398,168,1430 +20 10012751 . T C 937.77 . AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.56;QD=31.26;SOR=0.976 GT:AD:DP:GQ:PL:PP 1/1:0,30:30:89:966,89,0:978,92,0,1035,152,1067 +20 10013119 . C T 1011.77 . 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=17.15;ReadPosRankSum=0.336;SOR=0.405 GT:AD:DP:GQ:PL:PP 0/1:29,30:59:99:1040,0,936:1036,0,946,1186,1092,2252 +20 10013574 . G A 1050.77 . 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=15.23;ReadPosRankSum=0.789;SOR=1.675 GT:AD:DP:GQ:PL:PP 0/1:38,31:69:99:1079,0,1301:1083,0,1303,1258,1457,2689 +20 10014990 . C CAT 1237.73 . 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=16.29;ReadPosRankSum=-3.430e-01;SOR=0.403 GT:AD:DP:GQ:PL:PP 0/1:38,38:76:99:1275,0,1248:1280,0,1249,1454,1428,2856 +20 10015679 . C T 140.77 . 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=14.08;ReadPosRankSum=0.355;SOR=0.693 GT:AD:DP:GQ:PL:PP 0/1:5,5:10:99:169,0,166:166,0,175,242,246,461 +20 10015761 . T C 344.77 . 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=15.67;ReadPosRankSum=-4.250e-01;SOR=0.352 GT:AD:DP:GQ:PL:PP 0/1:9,13:22:99:373,0,284:377,0,286,464,386,822 +20 10018158 . G C 1639.77 . 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=18.63;ReadPosRankSum=0.516;SOR=0.834 GT:AD:DP:GQ:PL:PP 0/1:40,48:88:99:1668,0,1165:1672,0,1167,1852,1372,3197 +20 10018555 . G A 1567.77 . 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=19.60;ReadPosRankSum=0.463;SOR=0.627 GT:AD:DP:GQ:PL:PP 0/1:35,45:80:99:1596,0,1211:1593,0,1220,1761,1413,3147 +20 10019093 . A G 1244.77 . 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=18.04;ReadPosRankSum=-2.300e-01;SOR=0.665 GT:AD:DP:GQ:PL:PP 0/1:33,36:69:99:1273,0,1104:1277,0,1106,1436,1275,2685 +20 10020229 . G A 1538.77 . 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=18.77;ReadPosRankSum=-3.680e-01;SOR=0.573 GT:AD:DP:GQ:PL:PP 0/1:38,44:82:99:1567,0,1130:1564,0,1139,1742,1329,3043 +20 10023689 . G A 1852.77 . 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=23.16;ReadPosRankSum=0.764;SOR=0.549 GT:AD:DP:GQ:PL:PP 0/1:29,51:80:99:1881,0,946:1881,0,952,2030,1164,3167 +20 10024107 . C T 1694.77 . 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=19.71;ReadPosRankSum=0.329;SOR=0.823 GT:AD:DP:GQ:PL:PP 0/1:38,48:86:99:1723,0,1086:1659,0,1126,1837,1297,3108 +20 10024300 . C CTT 87.76 . 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=7.98;ReadPosRankSum=0.00;SOR=1.825 GT:AD:DP:GQ:PL:PP 0/1:3,8:18:99:103,0,137:39,56,428,15,214,168,8,64,0,184,141,334,247,162,365 +20 10026357 . T C 1166.77 . 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=18.52;ReadPosRankSum=-5.490e-01;SOR=0.722 GT:AD:DP:GQ:PL:PP 0/1:28,35:63:99:1195,0,932:1192,0,941,1339,1103,2415 +20 10026794 . C T 1084.77 . 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=20.86;ReadPosRankSum=-7.000e-02;SOR=0.428 GT:AD:DP:GQ:PL:PP 0/1:19,33:52:99:1113,0,529:1110,0,538,1230,693,1897 +20 10027234 . A ATTAG 1320.73 . 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=19.14;ReadPosRankSum=-9.310e-01;SOR=0.926 GT:AD:DP:GQ:PL:PP 0/1:34,35:69:99:1358,0,1964:1362,0,1966,1525,2132,3631 +20 10027868 . A G 1739.77 . 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=19.55;ReadPosRankSum=1.23;SOR=0.881 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:44,45:89:99:0|1:10027868_A_G:1768,0,3201:1765,0,3210,1961,3406,5339 +20 10027872 . A G 1724.77 . 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=20.29;ReadPosRankSum=0.173;SOR=0.826 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:40,45:85:99:0|1:10027868_A_G:1753,0,3136:1750,0,3145,1939,3338,5250 +20 10028867 . A ATG 1106.73 . 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=15.59;ReadPosRankSum=0.075;SOR=0.336 GT:AD:DP:GQ:PL:PP 0/1:32,39:71:99:1144,0,916:1138,0,928,1246,1046,2295 +20 10030188 . T A 1372.77 . 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=16.95;ReadPosRankSum=-1.072e+00;SOR=1.105 GT:AD:DP:GQ:PL:PP 0/1:42,39:81:99:1401,0,1524:1398,0,1533,1587,1707,3267 +20 10031254 . A AT 1463.73 . 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=17.22;ReadPosRankSum=0.478;SOR=0.211 GT:AD:DP:GQ:PL:PP 0/1:38,47:85:99:1501,0,1159:1498,0,1168,1676,1366,3015 +20 10031342 . G A 1834.77 . 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=19.73;ReadPosRankSum=-2.630e-01;SOR=0.955 GT:AD:DP:GQ:PL:PP 0/1:41,52:93:99:1863,0,1375:1867,0,1377,2050,1595,3618 +20 10031798 . G A 4296.77 . AC=2;AF=1.00;AN=2;DP=104;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;QD=31.54;SOR=0.900 GT:AD:DP:GQ:PL:PP 1/1:0,104:104:99:4325,313,0:4368,331,0,4410,377,4429 +20 10031827 . C T 2004.77 . 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=18.56;ReadPosRankSum=-3.900e-01;SOR=0.382 GT:AD:DP:GQ:PL:PP 0/1:52,56:108:99:2033,0,1798:2030,0,1807,2249,2032,4254 +20 10032094 . G A 1220.77 . 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=14.71;ReadPosRankSum=-4.640e-01;SOR=0.260 GT:AD:DP:GQ:PL:PP 0/1:47,36:83:99:1249,0,1497:1246,0,1506,1450,1671,3094 +20 10032413 . T G 869.77 . 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=13.18;ReadPosRankSum=-7.510e-01;SOR=1.293 GT:AD:DP:GQ:PL:PP 0/1:35,31:66:99:898,0,1277:895,0,1286,1063,1437,2473 +20 10032882 . A T 1202.77 . 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=16.04;ReadPosRankSum=0.579;SOR=0.338 GT:AD:DP:GQ:PL:PP 0/1:39,36:75:99:1231,0,1406:1236,0,1407,1413,1577,2963 +20 10032972 . C CAT 1122.73 . 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=17.82;ReadPosRankSum=-1.239e+00;SOR=1.300 GT:AD:DP:GQ:PL:PP 0/1:33,30:63:99:1160,0,1477:1165,0,1478,1325,1631,2928 +20 10034306 . T C 782.77 . 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=10.44;ReadPosRankSum=0.280;SOR=0.685 GT:AD:DP:GQ:PL:PP 0/1:46,29:75:99:811,0,1593:808,0,1602,1010,1746,2729 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1036.73 . 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=15.25;ReadPosRankSum=0.200;SOR=0.269 GT:AD:DP:GQ:PL:PP 0/1:39,29:68:99:1074,0,5571:1074,0,5577,1253,5730,6956 +20 10037037 . C T 1436.77 . 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=17.74;ReadPosRankSum=-1.694e+00;SOR=0.495 GT:AD:DP:GQ:PL:PP 0/1:39,42:81:99:1465,0,1124:1463,0,1132,1641,1317,2930 +20 10037110 . T TGATA 2780.73 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=28.86;SOR=1.022 GT:AD:DP:GQ:PL:PP 1/1:0,61:61:99:2818,189,0:2822,188,0,2883,252,2920 +20 10037144 . T TGATAGATA 1823.73 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=29.41;SOR=1.061 GT:AD:DP:GQ:PL:PP 1/1:0,36:36:99:1861,127,0:1848,118,0,1852,123,1860 +20 10037709 . A T 1003.77 . 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=14.14;ReadPosRankSum=0.600;SOR=0.608 GT:AD:DP:GQ:PL:PP 0/1:39,32:71:99:1032,0,1354:1029,0,1363,1210,1516,2699 +20 10039371 . T G 1324.77 . 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=17.90;ReadPosRankSum=0.510;SOR=1.031 GT:AD:DP:GQ:PL:PP 0/1:34,40:74:99:1353,0,1194:1350,0,1203,1515,1381,2869 +20 10040772 . C CT 1995.73 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.69;QD=28.51;SOR=0.811 GT:AD:DP:GQ:PL:PP 1/1:0,70:70:99:2033,210,0:2020,201,0,2032,215,2049 +20 10040812 . AT A 2607.73 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.73;QD=31.11;SOR=0.721 GT:AD:DP:GQ:PL:PP 1/1:0,71:71:99:2645,214,0:2637,207,0,2667,240,2701 +20 10040821 . T A 1171.77 . 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=15.02;ReadPosRankSum=-1.410e+00;SOR=0.688 GT:AD:DP:GQ:PL:PP 0/1:38,40:78:99:1200,0,1099:1194,0,1111,1372,1285,2630 +20 10041304 . C T 2765.77 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.40;QD=34.66;SOR=0.693 GT:AD:DP:GQ:PL:PP 1/1:0,68:68:99:2794,204,0:2795,201,0,2856,265,2892 +20 10041701 . A ATATG 1403.73 . 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=25.07;ReadPosRankSum=0.328;SOR=0.260 GT:AD:DP:GQ:PL:PP 0/1:8,48:56:58:1441,0,58:1441,1653,2834,0,335,64,1579,2395,271,2215 +20 10042319 . C T 2658.77 . AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=29.40;SOR=1.033 GT:AD:DP:GQ:PL:PP 1/1:0,66:66:99:2687,199,0:2697,201,0,2710,217,2730 +20 10042761 . A G 3553.77 . AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=36.76;SOR=1.389 GT:AD:DP:GQ:PL:PP 1/1:0,91:91:99:3582,272,0:3572,264,0,3635,330,3674 +20 10042829 . A G 3055.77 . AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;QD=30.54;SOR=0.855 GT:AD:DP:GQ:PL:PP 1/1:0,78:78:99:3084,235,0:3095,237,0,3152,298,3186 +20 10043002 . A T 1287.77 . 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=14.97;ReadPosRankSum=0.178;SOR=0.434 GT:AD:DP:GQ:PL:PP 0/1:48,38:86:99:1316,0,1659:1296,0,1685,1504,1840,3317 +20 10044849 . A G 2091.77 . AC=2;AF=1.00;AN=2;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=21.53;SOR=1.316 GT:AD:DP:GQ:PL:PP 1/1:0,59:59:99:2120,177,0:2109,168,0,2172,234,2211 +20 10045078 . G T 3271.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;QD=34.87;SOR=0.876 GT:AD:DP:GQ:PL:PP 1/1:0,81:81:99:3300,244,0:3298,240,0,3359,304,3397 +20 10045642 . G C 3107.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=31.04;SOR=0.821 GT:AD:DP:GQ:PL:PP 1/1:0,81:81:99:3136,243,0:3129,236,0,3191,302,3230 +20 10046178 . AAGAAAGAAAG A 2159.73 . AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.22;QD=27.86;SOR=0.859 GT:AD:DP:GQ:PL:PP 1/1:0,50:50:99:2197,152,0:2212,156,0,2268,215,2300 +20 10046537 . A G 819.77 . 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=14.38;ReadPosRankSum=0.412;SOR=1.262 GT:AD:DP:GQ:PL:PP 0/1:28,29:57:99:848,0,902:856,0,900,998,1049,2020 +20 10050828 . T C 1227.77 . 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=14.28;ReadPosRankSum=0.073;SOR=0.521 GT:AD:DP:GQ:PL:PP 0/1:49,37:86:99:1256,0,1768:1257,0,1773,1466,1944,3383 +20 10051448 . T C 1134.77 . 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=16.21;ReadPosRankSum=-5.490e-01;SOR=0.302 GT:AD:DP:GQ:PL:PP 0/1:35,35:70:99:1163,0,1150:1164,0,1155,1331,1320,2623 +20 10052688 . C A 1062.77 . 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=13.80;ReadPosRankSum=1.56;SOR=0.379 GT:AD:DP:GQ:PL:PP 0/1:45,32:77:99:1091,0,1645:1075,0,1667,1274,1808,3055 +20 10058022 . T C 975.77 . 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=14.35;ReadPosRankSum=-4.530e-01;SOR=0.849 GT:AD:DP:GQ:PL:PP 0/1:36,32:68:99:1004,0,1261:1001,0,1270,1172,1423,2568 +20 10062935 . C CA 92.84 . 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=6.19;ReadPosRankSum=-4.930e-01;SOR=0.446 GT:AD:DP:GQ:PL:PP 0/1:5,10:23:99:130,0,101:57,219,1863,163,1247,1084,115,704,652,545,0,234,158,92,141,234,1053,954,675,238,919 +20 10067049 . TAAAAAAAA T,TA 613.73 . 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=34.10;ReadPosRankSum=-4.960e-01;SOR=1.127 GT:AD:DP:GQ:PL:PP 1/2:2,7,9:22:99:651,164,340,135,0,106:573,291,860,90,313,275,128,101,0,138,427,582,385,229,650 +20 10067090 . C A 2004.77 . AC=2;AF=1.00;AN=2;DP=56;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.57;QD=34.17;SOR=0.729 GT:AD:DP:GQ:PL:PP 1/1:0,55:55:99:2033,164,0:2035,162,0,2096,226,2132 +20 10067264 . G A 2922.77 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.37;QD=28.60;SOR=0.776 GT:AD:DP:GQ:PL:PP 1/1:0,73:73:99:2951,219,0:2946,214,0,3008,279,3046 +20 10067722 . A C 2146.77 . AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.57;SOR=0.846 GT:AD:DP:GQ:PL:PP 1/1:0,54:54:99:2175,163,0:2177,161,0,2237,224,2274 +20 10068158 . GTGTATATATATA G 66.73 . 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=9.53;ReadPosRankSum=-2.530e-01;SOR=0.061 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:3,4:7:57:0|1:10068158_GTGTATATATATA_G:104,0,57:31,0,97,105,136,214 +20 10068981 . G A 2503.77 . AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.11;SOR=0.941 GT:AD:DP:GQ:PL:PP 1/1:0,61:61:99:2532,184,0:2533,182,0,2594,245,2631 +20 10070602 . T C 2691.77 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.74;QD=30.20;SOR=0.749 GT:AD:DP:GQ:PL:PP 1/1:0,72:72:99:2720,216,0:2693,199,0,2757,266,2797 +20 10070936 . T A 3631.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.76;QD=30.49;SOR=0.876 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,81:81:99:1|1:10070936_T_A:3660,247,0:3649,239,0,3712,305,3751 +20 10070938 . G GA 3656.73 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.10;QD=31.67;SOR=0.881 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,79:79:99:1|1:10070936_T_A:3694,250,0:3683,242,0,3746,308,3785 +20 10071135 . C T 3257.77 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=29.53;SOR=1.003 GT:AD:DP:GQ:PL:PP 1/1:0,79:79:99:3286,238,0:3300,242,0,3356,301,3389 +20 10071187 . G A 3410.77 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;QD=32.63;SOR=1.367 GT:AD:DP:GQ:PL:PP 1/1:0,82:82:99:3439,246,0:3427,237,0,3490,303,3529 +20 10071890 . T C 1974.77 . AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=34.65;SOR=0.728 GT:AD:DP:GQ:PL:PP 1/1:0,57:57:99:2003,171,0:1991,162,0,2054,228,2093 +20 10072505 . A G 2099.77 . AC=2;AF=1.00;AN=2;DP=64;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.81;SOR=0.822 GT:AD:DP:GQ:PL:PP 1/1:0,64:64:99:2128,191,0:2101,174,0,2164,241,2204 +20 10074187 . A G 3101.77 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.12;QD=30.36;SOR=0.881 GT:AD:DP:GQ:PL:PP 1/1:0,79:79:99:3130,238,0:3114,227,0,3177,293,3217 +20 10074240 . T C 3406.77 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=28.13;SOR=0.922 GT:AD:DP:GQ:PL:PP 1/1:0,85:85:99:3435,255,0:3448,258,0,3504,318,3537 +20 10074716 . G A 2400.77 . AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;QD=27.97;SOR=1.214 GT:AD:DP:GQ:PL:PP 1/1:0,64:64:99:2429,192,0:2426,187,0,2487,252,2525 +20 10074806 . G A 2817.77 . AC=2;AF=1.00;AN=2;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=28.31;SOR=0.840 GT:AD:DP:GQ:PL:PP 1/1:0,71:71:99:2846,213,0:2833,204,0,2896,270,2936 +20 10075043 . T C 2405.77 . AC=2;AF=1.00;AN=2;DP=62;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.63;QD=35.21;SOR=1.107 GT:AD:DP:GQ:PL:PP 1/1:0,61:61:99:2434,184,0:2448,188,0,2504,247,2536 +20 10075168 . C T 3612.77 . AC=2;AF=1.00;AN=2;DP=88;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=35.18;SOR=0.997 GT:AD:DP:GQ:PL:PP 1/1:0,88:88:99:3641,264,0:3631,256,0,3694,322,3733 +20 10075508 . GA G 1928.73 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.17;QD=27.55;SOR=1.085 GT:AD:DP:GQ:PL:PP 1/1:0,70:70:99:1966,210,0:1963,205,0,1972,217,1987 +20 10076250 . A G 1107.77 . 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=14.02;ReadPosRankSum=-6.050e-01;SOR=0.344 GT:AD:DP:GQ:PL:PP 0/1:40,39:79:99:1136,0,1339:1143,0,1338,1323,1517,2812 +20 10076339 . A G 1309.77 . 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=18.19;ReadPosRankSum=0.508;SOR=0.446 GT:AD:DP:GQ:PL:PP 0/1:32,40:72:99:1338,0,1035:1345,0,1034,1501,1218,2690 +20 10076399 . G A 1807.77 . 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=19.23;ReadPosRankSum=-8.630e-01;SOR=0.952 GT:AD:DP:GQ:PL:PP 0/1:44,50:94:99:1836,0,1544:1843,0,1543,2034,1756,3763 +20 10076989 . CA C 214.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.500e-01;ClippingRankSum=0.00;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.16;MQRankSum=-4.630e-01;QD=10.74;ReadPosRankSum=-1.960e-01;SOR=0.495 GT:AD:DP:GQ:PL:PP 0/1:7,13:31:99:211,0,335:140,230,1143,0,482,373,106,310,34,358,210,675,386,281,600 +20 10077752 . T C 1345.77 . 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=17.04;ReadPosRankSum=-1.420e-01;SOR=1.251 GT:AD:DP:GQ:PL:PP 0/1:34,45:79:99:1374,0,1187:1362,0,1205,1528,1389,2890 +20 10079476 . T G 11.12 . 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=0.25;ReadPosRankSum=-4.313e+00;SOR=4.970 GT:AD:DP:GQ:PL:PP 0/1:33,11:44:39:39,0,1137:23,0,1159,185,1233,1392 +20 10081750 . C A 1353.77 . 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=16.31;ReadPosRankSum=-6.260e-01;SOR=0.664 GT:AD:DP:GQ:PL:PP 0/1:44,39:83:99:1382,0,1525:1381,0,1532,1576,1708,3257 +20 10081800 . C T 1109.77 . 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=16.32;ReadPosRankSum=-1.082e+00;SOR=0.143 GT:AD:DP:GQ:PL:PP 0/1:35,33:68:99:1138,0,1222:1138,0,1229,1306,1387,2665 +20 10082892 . C T 1712.77 . AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=29.59;SOR=0.883 GT:AD:DP:GQ:PGT:PID:PL:PP 1/1:0,44:44:99:1|1:10082885_A_C:1741,132,0:1749,133,0,1808,195,1842 +20 10085211 . A T 1210.77 . 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=15.93;ReadPosRankSum=-2.800e-01;SOR=0.723 GT:AD:DP:GQ:PL:PP 0/1:40,36:76:99:1239,0,1443:1236,0,1452,1420,1617,3010 +20 10086110 . G A 1274.77 . 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=15.74;ReadPosRankSum=0.875;SOR=0.495 GT:AD:DP:GQ:PL:PP 0/1:43,38:81:99:1303,0,1506:1311,0,1504,1498,1682,3153 +20 10086283 . G T 1025.77 . 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=12.21;ReadPosRankSum=1.61;SOR=0.529 GT:AD:DP:GQ:PL:PP 0/1:52,32:84:99:1054,0,1771:1062,0,1769,1276,1928,3177 +20 10086619 . T A 796.77 . 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=11.38;ReadPosRankSum=-5.100e-02;SOR=0.846 GT:AD:DP:GQ:PL:PP 0/1:45,25:70:99:825,0,1603:819,0,1615,1019,1745,2736 +20 10086853 . G A 1002.77 . 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=13.74;ReadPosRankSum=-2.700e-01;SOR=0.767 GT:AD:DP:GQ:PL:PP 0/1:41,32:73:99:1031,0,1280:1039,0,1278,1220,1437,2630 +20 10086954 . G A 1095.77 . 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=16.11;ReadPosRankSum=-8.120e-01;SOR=1.185 GT:AD:DP:GQ:PL:PP 0/1:34,34:68:99:1124,0,1051:1132,0,1049,1292,1214,2480 +20 10087230 . A G 1842.77 . 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=19.20;ReadPosRankSum=0.893;SOR=0.960 GT:AD:DP:GQ:PL:PP 0/1:42,54:96:99:1871,0,1428:1879,0,1426,2064,1651,3688 +20 10087394 . T G 1688.77 . 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=20.10;ReadPosRankSum=1.18;SOR=0.436 GT:AD:DP:GQ:PL:PP 0/1:35,49:84:99:1717,0,1186:1711,0,1198,1881,1400,3253 +20 10087754 . T G 1347.77 . 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=17.28;ReadPosRankSum=-8.310e-01;SOR=0.562 GT:AD:DP:GQ:PL:PP 0/1:37,41:78:99:1376,0,1239:1373,0,1248,1548,1428,2948 +20 10087804 . C T 1619.77 . 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=16.20;ReadPosRankSum=1.02;SOR=0.369 GT:AD:DP:GQ:PL:PP 0/1:50,50:100:99:1648,0,1511:1656,0,1509,1863,1722,3558 +20 10087820 . C CAG 428.73 . 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=8.09;ReadPosRankSum=-9.000e-03;SOR=0.850 GT:AD:DP:GQ:PL:PP 0/1:35,18:53:99:466,0,1168:464,736,2681,0,1269,1176,656,2304,1238,2187 +20 10088063 . C T 1417.77 . 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=15.24;ReadPosRankSum=0.354;SOR=1.053 GT:AD:DP:GQ:PL:PP 0/1:49,44:93:99:1446,0,1403:1454,0,1401,1658,1596,3228 +20 10088699 . C T 776.77 . 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=12.53;ReadPosRankSum=-5.770e-01;SOR=1.914 GT:AD:DP:GQ:PL:PP 0/1:36,26:62:99:805,0,1088:813,0,1086,979,1227,2179 +20 10088730 . G A 972.77 . 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=18.71;ReadPosRankSum=0.433;SOR=1.592 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:29,23:52:99:0|1:10088730_G_A:1001,0,1152:1009,0,1150,1158,1292,2422 +20 10088736 . A C 1081.77 . 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=19.67;ReadPosRankSum=-4.200e-02;SOR=0.851 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:28,27:55:99:0|1:10088730_G_A:1110,0,1194:1118,0,1192,1269,1342,2584 +20 10088747 . A G 1111.77 . 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=20.59;ReadPosRankSum=-3.390e-01;SOR=1.092 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:25,29:54:99:0|1:10088730_G_A:1140,0,995:1147,0,994,1285,1146,2404 +20 10088799 . G A 1018.77 . 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=19.22;ReadPosRankSum=1.35;SOR=1.003 GT:AD:DP:GQ:PL:PP 0/1:22,31:53:99:1047,0,617:1056,0,614,1180,771,1923 +20 10088895 . C T 532.77 . 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=12.99;ReadPosRankSum=0.907;SOR=0.653 GT:AD:DP:GQ:PL:PP 0/1:23,18:41:99:561,0,673:568,0,672,696,787,1456 +20 10088968 . C CAAA 1175.73 . 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=22.18;ReadPosRankSum=1.02;SOR=1.012 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367:1218,0,1368,1318,1469,2790 +20 10088980 . T C 1247.77 . 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=18.35;ReadPosRankSum=0.999;SOR=0.709 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627:1284,0,1625,1460,1790,3223 +20 10088985 . T C 1178.77 . 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=15.93;ReadPosRankSum=1.38;SOR=0.742 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729:1215,0,1727,1399,1887,3259 +20 10089441 . A G 1179.77 . 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=15.52;ReadPosRankSum=0.161;SOR=1.363 GT:AD:DP:GQ:PL:PP 0/1:37,39:76:99:1208,0,1313:1206,0,1322,1379,1496,2848 +20 10089525 . C T 1548.77 . 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=19.12;ReadPosRankSum=0.428;SOR=0.617 GT:AD:DP:GQ:PL:PP 0/1:38,43:81:99:1577,0,1088:1585,0,1086,1757,1278,3008 +20 10090289 . CA C 384.73 . 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=11.32;ReadPosRankSum=-2.230e-01;SOR=0.859 GT:AD:DP:GQ:PL:PP 0/1:14,20:38:99:422,0,230:423,357,984,0,259,235,537,926,410,1023 +20 10090764 . A G 840.77 . 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=13.35;ReadPosRankSum=0.695;SOR=0.310 GT:AD:DP:GQ:PL:PP 0/1:34,29:63:99:869,0,1207:880,0,1202,1038,1352,2363 +20 10090970 . T C 1257.77 . 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=18.23;ReadPosRankSum=0.429;SOR=0.518 GT:AD:DP:GQ:PL:PP 0/1:33,36:69:99:1286,0,1092:1285,0,1099,1446,1267,2685 +20 10091214 . C T 1249.77 . 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=17.85;ReadPosRankSum=0.392;SOR=0.625 GT:AD:DP:GQ:PL:PP 0/1:33,37:70:99:1278,0,1110:1275,0,1119,1437,1288,2698 +20 10092415 . A G 1635.77 . 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=16.20;ReadPosRankSum=-7.000e-02;SOR=0.665 GT:AD:DP:GQ:PL:PP 0/1:52,49:101:99:1664,0,1902:1661,0,1911,1880,2115,3969 +20 10092927 . G T 106.77 . 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=1.48;ReadPosRankSum=-4.416e+00;SOR=5.279 GT:AD:DP:GQ:PL:PP 0/1:59,13:72:99:135,0,1864:123,0,1882,362,1968,2303 +20 10093568 . GT G 326.73 . 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=9.61;ReadPosRankSum=0.987;SOR=0.751 GT:AD:DP:GQ:PL:PP 0/1:17,17:42:99:364,0,386:365,399,1228,0,502,391,447,852,365,1015,429,908,449,850,886 +20 10093923 . T A 1075.77 . 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=16.06;ReadPosRankSum=-2.256e+00;SOR=0.772 GT:AD:DP:GQ:PL:PP 0/1:35,32:67:99:1104,0,1257:1101,0,1266,1269,1419,2662 +20 10094251 . T A 1270.77 . 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=20.50;ReadPosRankSum=1.73;SOR=1.211 GT:AD:DP:GQ:PL:PP 0/1:26,36:62:99:1299,0,781:1296,0,790,1436,955,2364 +20 10094582 . A G 923.77 . 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=13.39;ReadPosRankSum=-5.270e-01;SOR=0.772 GT:AD:DP:GQ:PL:PP 0/1:39,30:69:99:952,0,1350:932,0,1376,1114,1507,2594 +20 10094774 . C T 1036.77 . 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=13.82;ReadPosRankSum=0.494;SOR=0.690 GT:AD:DP:GQ:PL:PP 0/1:40,35:75:99:1065,0,1282:1062,0,1291,1245,1451,2669 +20 10095432 . GTGATGATGA G 839.73 . 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=16.79;ReadPosRankSum=0.660;SOR=0.460 GT:AD:DP:GQ:PL:PP 0/1:27,23:50:99:877,0,2108:880,0,2111,956,2178,3137 +20 10095741 . A G 1075.77 . 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=15.37;ReadPosRankSum=-3.260e-01;SOR=0.515 GT:AD:DP:GQ:PL:PP 0/1:36,34:70:99:1104,0,1233:1103,0,1240,1275,1401,2647 +20 10096293 . C T 1355.77 . 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=18.08;ReadPosRankSum=0.012;SOR=0.638 GT:AD:DP:GQ:PL:PP 0/1:37,38:75:99:1384,0,1258:1381,0,1267,1555,1438,2966 +20 10096596 . C T 1562.77 . 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=17.96;ReadPosRankSum=0.166;SOR=0.640 GT:AD:DP:GQ:PL:PP 0/1:40,47:87:99:1591,0,1273:1589,0,1281,1772,1480,3225 +20 10096768 . A C 1682.77 . 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=18.49;ReadPosRankSum=0.541;SOR=0.445 GT:AD:DP:GQ:PL:PP 0/1:42,49:91:99:1711,0,1452:1720,0,1449,1904,1660,3536 +20 10096899 . G T 1614.77 . 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=20.44;ReadPosRankSum=0.378;SOR=1.707 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:39,40:79:99:0|1:10096899_G_T:1643,0,1520:1652,0,1517,1830,1709,3512 +20 10096905 . TA T 1600.73 . 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=19.29;ReadPosRankSum=0.397;SOR=1.775 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:40,43:83:99:0|1:10096899_G_T:1638,0,1623:1647,0,1620,1834,1812,3619 +20 10096933 . G C 1511.77 . 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=17.79;ReadPosRankSum=0.238;SOR=1.534 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:44,41:85:99:0|1:10096933_G_C:1540,0,1770:1549,0,1767,1750,1956,3679 +20 10096958 . G A 1766.77 . 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=19.20;ReadPosRankSum=-1.860e+00;SOR=1.387 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:45,47:92:99:0|1:10096933_G_C:1795,0,1629:1805,0,1625,1995,1832,3800 +20 10097075 . T G 1445.77 . 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=15.71;ReadPosRankSum=-2.850e-01;SOR=0.628 GT:AD:DP:GQ:PL:PP 0/1:44,48:92:99:1474,0,1482:1483,0,1479,1672,1686,3331 +20 10097101 . C CTTT 1091.73 . 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=18.20;ReadPosRankSum=1.11;SOR=0.277 GT:AD:DP:GQ:PL:PP 0/1:34,26:64:99:1129,0,1306:1130,0,1311,554,1322,2009,1042,1492,2110,2472 +20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1054.73 . 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=11.85;ReadPosRankSum=-3.231e+00;SOR=0.948 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:57,32:89:99:0|1:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:1092,0,2241:1019,0,2281,1254,2405,3632 +20 10097437 . TTTTC T 796.73 . 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=14.49;ReadPosRankSum=2.93;SOR=1.382 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:32,23:55:99:1|0:10097436_CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT_C:834,0,1193:832,0,1201,919,1256,2178 +20 10097626 . C A 626.77 . 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=13.06;ReadPosRankSum=1.15;SOR=0.324 GT:AD:DP:GQ:PL:PP 0/1:28,20:48:99:655,0,957:653,0,965,800,1083,1856 +20 10097789 . T C 688.77 . 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=12.08;ReadPosRankSum=-9.200e-02;SOR=0.756 GT:AD:DP:GQ:PL:PP 0/1:34,23:57:99:717,0,1190:726,0,1187,886,1320,2178 +20 10097928 . G A 570.77 . 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=15.85;ReadPosRankSum=0.057;SOR=0.951 GT:AD:DP:GQ:PL:PP 0/1:17,19:36:99:599,0,586:609,0,583,716,703,1392 +20 10098110 . G C 586.77 . 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=16.30;ReadPosRankSum=-7.140e-01;SOR=0.069 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:19,17:36:99:0|1:10098110_G_C:615,0,727:625,0,723,738,838,1549 +20 10098135 . C A 471.77 . 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=12.41;ReadPosRankSum=-7.690e-01;SOR=0.075 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:24,14:38:99:0|1:10098110_G_C:500,0,964:510,0,960,641,1065,1680 +20 10098219 . TATATATA T 295.73 . 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=14.08;ReadPosRankSum=0.498;SOR=0.465 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:12,9:21:99:0|1:10098219_TATATATA_T:333,0,461:342,0,458,435,548,957 +20 10098237 . A T 244.77 . 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=18.83;ReadPosRankSum=0.277;SOR=0.836 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:6,7:13:99:0|1:10098219_TATATATA_T:273,0,273:274,0,278,357,359,688 +20 10098265 . T C 133.77 . 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=22.29;ReadPosRankSum=0.00;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:2,4:6:59:0|1:10098219_TATATATA_T:162,0,59:98,0,99,168,138,279 +20 10098885 . C CA 433.73 . 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=13.99;ReadPosRankSum=-1.590e-01;SOR=0.518 GT:AD:DP:GQ:PL:PP 0/1:17,14:31:99:471,0,572:479,0,570,588,674,1236 +20 10098945 . T C 452.77 . 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=20.58;ReadPosRankSum=0.837;SOR=2.368 GT:AD:DP:GQ:PL:PP 0/1:9,13:22:99:481,0,248:489,0,246,573,348,893 +20 10098987 . C T 379.77 . 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=15.82;ReadPosRankSum=0.348;SOR=2.925 GT:AD:DP:GQ:PL:PP 0/1:11,13:24:99:408,0,350:401,0,363,497,455,925 +20 10099029 . T C 334.77 . 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=11.96;ReadPosRankSum=-7.930e-01;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:18,10:28:99:0|1:10099029_T_C:363,0,768:373,0,765,486,858,1317 +20 10099034 . C A 334.77 . 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=11.96;ReadPosRankSum=-1.540e+00;SOR=1.721 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:18,10:28:99:0|1:10099029_T_C:363,0,768:373,0,765,486,858,1317 +20 10099044 . A C 334.77 . 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=13.95;ReadPosRankSum=-2.625e+00;SOR=0.515 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:15,9:24:99:0|1:10099029_T_C:363,0,768:373,0,765,486,858,1317 +20 10099046 . T C 304.77 . 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=12.70;ReadPosRankSum=-2.686e+00;SOR=0.515 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:15,9:24:99:0|1:10099029_T_C:333,0,603:343,0,600,444,690,1107 +20 10099055 . T C 256.77 . 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=11.16;ReadPosRankSum=-2.131e+00;SOR=0.665 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:15,8:23:99:0|1:10099029_T_C:285,0,673:295,0,670,402,757,1132 +20 10099079 . C T 116.77 . 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=4.03;ReadPosRankSum=1.97;SOR=1.289 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:23,6:29:99:0|1:10099029_T_C:145,0,886:155,0,883,283,964,1219 +20 10099111 . T TTTTGTTTG 656.73 . 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=18.76;ReadPosRankSum=-1.200e-01;SOR=0.511 GT:AD:DP:GQ:PL:PP 0/1:22,13:35:99:694,0,802:700,0,802,791,883,1676 +20 10099140 . G T 1005.77 . 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=16.22;ReadPosRankSum=0.169;SOR=1.114 GT:AD:DP:GQ:PL:PP 0/1:30,32:62:99:1034,0,931:1043,0,928,1188,1088,2249 +20 10099190 . G T 1034.77 . 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=15.92;ReadPosRankSum=-1.418e+00;SOR=0.776 GT:AD:DP:GQ:PL:PP 0/1:33,32:65:99:1063,0,1154:1072,0,1151,1228,1311,2512 +20 10099220 . A G 577.77 . 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=12.84;ReadPosRankSum=0.331;SOR=0.519 GT:AD:DP:GQ:PL:PP 0/1:25,20:45:99:606,0,873:616,0,869,747,992,1712 +20 10099250 . G A 699.77 . 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=18.91;ReadPosRankSum=0.169;SOR=0.162 GT:AD:DP:GQ:PL:PP 0/1:16,21:37:99:728,0,424:725,0,433,836,553,1362 +20 10099535 . G A 1335.77 . 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=20.55;ReadPosRankSum=-5.080e-01;SOR=0.408 GT:AD:DP:GQ:PL:PP 0/1:26,39:65:99:1364,0,686:1373,0,683,1508,863,2344 +20 10099565 . C T 1346.77 . 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=19.52;ReadPosRankSum=0.740;SOR=0.191 GT:AD:DP:GQ:PL:PP 0/1:31,38:69:99:1375,0,994:1384,0,991,1534,1168,2675 +20 10099755 . C T 1098.77 . 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=16.90;ReadPosRankSum=-6.840e-01;SOR=0.446 GT:AD:DP:GQ:PL:PP 0/1:33,32:65:99:1127,0,1148:1136,0,1145,1292,1305,2569 +20 10099832 . A G 1073.77 . 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=14.91;ReadPosRankSum=0.213;SOR=0.871 GT:AD:DP:GQ:PL:PP 0/1:39,33:72:99:1102,0,1430:1113,0,1425,1286,1588,2847 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testDefaultsWithPanel.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testDefaultsWithPanel.vcf new file mode 100644 index 00000000000..d4363fe1569 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testDefaultsWithPanel.vcf @@ -0,0 +1,44 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/rocCurve/2.3-174/.queue/scatterGather/call.and.assess.NA12878-1-sg/temp_64_of_80/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=120 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null 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 logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub graphOutput=null pair_hmm_implementation=LOGLESS_CACHING keepRG=null minPruning=2 gcpHMM=10 minKmer=11 downsampleRegion=1000 useAllelesTrigger=false useFilteredReadsForAnnotations=false dbsnp=(RodBinding name= source=UNBOUND) comp=[] annotation=[ClippingRankSumTest] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=0.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.05 logRemovedReadsFromContaminationFiltering=null exactcallslog=null debug=false activeRegionOut=null activeRegionIn=null filter_mismatching_base_and_quals=false" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[20:10000000-15000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null 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 logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/rocCurve/chr20.5mb.NA12878.2.3-174.hc.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false regenotype=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_mismatching_base_and_quals=false" +##contig= +##contig= +##reference=human_g1k_v37.fasta +##source=SelectVariants +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10001436 . A AAGGCT 3862.77 . AC=2;AF=1.00;AN=2;DP=48;FS=0.000;HaplotypeScore=9.1318;MLEAC=2;MLEAF=1.00;MQ=42.54;MQ0=0;PG=11,3,0;QD=16.09 GT:AD:GQ:PL:PP 1/1:0,43:99:3891,154,0:3902,157,0 +20 10002458 . G GTTT,GT 756.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=51;FS=0.000;HaplotypeScore=46.1412;MLEAC=1,1;MLEAF=0.500,0.500;MQ=52.11;MQ0=0;PG=0,34,71,34,71,71;QD=7.41 GT:AD:GQ:PL:PP 1/2:0,20,6:99:3411,302,122,899,0,719:3340,265,122,862,0,719 +20 10004223 . A AG 1611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;ClippingRankSum=-2.330;DP=66;FS=0.000;HaplotypeScore=85.7780;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=0;MQRankSum=3.605;PG=0,13,31;QD=24.42;ReadPosRankSum=2.345 GT:AD:GQ:PL:PP 0/1:31,28:99:1640,0,1329:1627,0,1348 +20 10004769 . TAAAACTATGC T 3929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.015;ClippingRankSum=-0.803;DP=79;FS=6.987;HaplotypeScore=16.2718;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-5.938;PG=0,5,15;QD=4.97;ReadPosRankSum=3.465 GT:AD:GQ:PL:PP 0/1:46,26:99:3958,0,5569:3953,0,5580 +20 10006819 . AAAAC A 3457.77 . AC=2;AF=1.00;AN=2;DP=77;FS=0.000;HaplotypeScore=22.5175;MLEAC=2;MLEAF=1.00;MQ=60.82;MQ0=0;PG=11,3,0;QD=11.23 GT:AD:GQ:PL:PP 1/1:0,59:99:3486,178,0:3497,181,0 +20 10008029 . T TA 2579.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.933;ClippingRankSum=0.500;DP=89;FS=0.000;HaplotypeScore=21.5461;MLEAC=2;MLEAF=1.00;MQ=60.92;MQ0=0;MQRankSum=0.122;PG=9,2,0;QD=28.99;ReadPosRankSum=-1.068 GT:AD:GQ:PL:PP 1/1:3,72:99:2608,223,0:2617,225,0 +20 10008146 . TA T 10964.77 . AC=2;AF=1.00;AN=2;DP=74;FS=0.000;HaplotypeScore=24.1439;MLEAC=2;MLEAF=1.00;MQ=60.27;MQ0=0;PG=13,3,0;QD=148.17 GT:AD:GQ:PL:PP 1/1:0,70:99:10993,805,0:11006,808,0 +20 10008758 . C CA 1819.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.813;ClippingRankSum=-1.164;DP=51;FS=4.935;HaplotypeScore=90.2830;MLEAC=2;MLEAF=1.00;MQ=33.83;MQ0=1;MQRankSum=-0.286;PG=3,0,3;QD=35.68;ReadPosRankSum=-0.505 GT:AD:GQ:PL:PP 1/1:4,37:99:1848,126,0:1848,123,0 +20 10008950 . AACACACACACAC A,AACACACACAC 2650.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.622;ClippingRankSum=-0.403;DP=58;FS=0.000;HaplotypeScore=137.9823;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.36;MQ0=0;MQRankSum=0.549;PG=0,0,0,0,0,0;QD=6.53;ReadPosRankSum=0.195 GT:AD:GQ:PL:PP 1/2:2,15,17:99:3592,904,2216,1963,0,1831:3592,904,2216,1963,0,1831 +20 10009882 . GAGAAGAA G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.105;ClippingRankSum=3.616;DP=57;FS=3.656;HaplotypeScore=75.0802;MLEAC=1;MLEAF=0.500;MQ=51.53;MQ0=1;MQRankSum=-1.230;PG=0,0,0;QD=0.92;ReadPosRankSum=-2.583 GT:AD:GQ:PL:PP 0/1:46,8:99:396,0,7299:396,0,7299 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testInputINDELs.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testInputINDELs.vcf index 799fceba2d1..d4363fe1569 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testInputINDELs.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testInputINDELs.vcf @@ -32,13 +32,13 @@ ##reference=human_g1k_v37.fasta ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -20 10001436 . A AAGGCT 3862.77 . AC=2;AF=1.00;AN=2;DP=48;FS=0.000;HaplotypeScore=9.1318;MLEAC=2;MLEAF=1.00;MQ=42.54;MQ0=0;PG=0,0,0;QD=16.09 GT:AD:GQ:PL:PP 1/1:0,43:99:3891,154,0:3891,154,0 -20 10002458 . G GTTT,GT 756.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=51;FS=0.000;HaplotypeScore=46.1412;MLEAC=1,1;MLEAF=0.500,0.500;MQ=52.11;MQ0=0;PG=0,0,0,0,0,0;QD=7.41 GT:AD:GQ:PL:PP 1/2:0,20,6:99:3411,302,122,899,0,719:3411,302,122,899,0,719 -20 10004223 . A AG 1611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;ClippingRankSum=-2.330;DP=66;FS=0.000;HaplotypeScore=85.7780;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=0;MQRankSum=3.605;PG=0,0,0;QD=24.42;ReadPosRankSum=2.345 GT:AD:GQ:PL:PP 0/1:31,28:99:1640,0,1329:1640,0,1329 -20 10004769 . TAAAACTATGC T 3929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.015;ClippingRankSum=-0.803;DP=79;FS=6.987;HaplotypeScore=16.2718;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-5.938;PG=0,0,0;QD=4.97;ReadPosRankSum=3.465 GT:AD:GQ:PL:PP 0/1:46,26:99:3958,0,5569:3958,0,5569 -20 10006819 . AAAAC A 3457.77 . AC=2;AF=1.00;AN=2;DP=77;FS=0.000;HaplotypeScore=22.5175;MLEAC=2;MLEAF=1.00;MQ=60.82;MQ0=0;PG=0,0,0;QD=11.23 GT:AD:GQ:PL:PP 1/1:0,59:99:3486,178,0:3486,178,0 -20 10008029 . T TA 2579.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.933;ClippingRankSum=0.500;DP=89;FS=0.000;HaplotypeScore=21.5461;MLEAC=2;MLEAF=1.00;MQ=60.92;MQ0=0;MQRankSum=0.122;PG=0,0,0;QD=28.99;ReadPosRankSum=-1.068 GT:AD:GQ:PL:PP 1/1:3,72:99:2608,223,0:2608,223,0 -20 10008146 . TA T 10964.77 . AC=2;AF=1.00;AN=2;DP=74;FS=0.000;HaplotypeScore=24.1439;MLEAC=2;MLEAF=1.00;MQ=60.27;MQ0=0;PG=0,0,0;QD=148.17 GT:AD:GQ:PL:PP 1/1:0,70:99:10993,805,0:10993,805,0 -20 10008758 . C CA 1819.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.813;ClippingRankSum=-1.164;DP=51;FS=4.935;HaplotypeScore=90.2830;MLEAC=2;MLEAF=1.00;MQ=33.83;MQ0=1;MQRankSum=-0.286;PG=0,0,0;QD=35.68;ReadPosRankSum=-0.505 GT:AD:GQ:PL:PP 1/1:4,37:99:1848,126,0:1848,126,0 +20 10001436 . A AAGGCT 3862.77 . AC=2;AF=1.00;AN=2;DP=48;FS=0.000;HaplotypeScore=9.1318;MLEAC=2;MLEAF=1.00;MQ=42.54;MQ0=0;PG=11,3,0;QD=16.09 GT:AD:GQ:PL:PP 1/1:0,43:99:3891,154,0:3902,157,0 +20 10002458 . G GTTT,GT 756.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=51;FS=0.000;HaplotypeScore=46.1412;MLEAC=1,1;MLEAF=0.500,0.500;MQ=52.11;MQ0=0;PG=0,34,71,34,71,71;QD=7.41 GT:AD:GQ:PL:PP 1/2:0,20,6:99:3411,302,122,899,0,719:3340,265,122,862,0,719 +20 10004223 . A AG 1611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;ClippingRankSum=-2.330;DP=66;FS=0.000;HaplotypeScore=85.7780;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=0;MQRankSum=3.605;PG=0,13,31;QD=24.42;ReadPosRankSum=2.345 GT:AD:GQ:PL:PP 0/1:31,28:99:1640,0,1329:1627,0,1348 +20 10004769 . TAAAACTATGC T 3929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.015;ClippingRankSum=-0.803;DP=79;FS=6.987;HaplotypeScore=16.2718;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-5.938;PG=0,5,15;QD=4.97;ReadPosRankSum=3.465 GT:AD:GQ:PL:PP 0/1:46,26:99:3958,0,5569:3953,0,5580 +20 10006819 . AAAAC A 3457.77 . AC=2;AF=1.00;AN=2;DP=77;FS=0.000;HaplotypeScore=22.5175;MLEAC=2;MLEAF=1.00;MQ=60.82;MQ0=0;PG=11,3,0;QD=11.23 GT:AD:GQ:PL:PP 1/1:0,59:99:3486,178,0:3497,181,0 +20 10008029 . T TA 2579.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.933;ClippingRankSum=0.500;DP=89;FS=0.000;HaplotypeScore=21.5461;MLEAC=2;MLEAF=1.00;MQ=60.92;MQ0=0;MQRankSum=0.122;PG=9,2,0;QD=28.99;ReadPosRankSum=-1.068 GT:AD:GQ:PL:PP 1/1:3,72:99:2608,223,0:2617,225,0 +20 10008146 . TA T 10964.77 . AC=2;AF=1.00;AN=2;DP=74;FS=0.000;HaplotypeScore=24.1439;MLEAC=2;MLEAF=1.00;MQ=60.27;MQ0=0;PG=13,3,0;QD=148.17 GT:AD:GQ:PL:PP 1/1:0,70:99:10993,805,0:11006,808,0 +20 10008758 . C CA 1819.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.813;ClippingRankSum=-1.164;DP=51;FS=4.935;HaplotypeScore=90.2830;MLEAC=2;MLEAF=1.00;MQ=33.83;MQ0=1;MQRankSum=-0.286;PG=3,0,3;QD=35.68;ReadPosRankSum=-0.505 GT:AD:GQ:PL:PP 1/1:4,37:99:1848,126,0:1848,123,0 20 10008950 . AACACACACACAC A,AACACACACAC 2650.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.622;ClippingRankSum=-0.403;DP=58;FS=0.000;HaplotypeScore=137.9823;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.36;MQ0=0;MQRankSum=0.549;PG=0,0,0,0,0,0;QD=6.53;ReadPosRankSum=0.195 GT:AD:GQ:PL:PP 1/2:2,15,17:99:3592,904,2216,1963,0,1831:3592,904,2216,1963,0,1831 20 10009882 . GAGAAGAA G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.105;ClippingRankSum=3.616;DP=57;FS=3.656;HaplotypeScore=75.0802;MLEAC=1;MLEAF=0.500;MQ=51.53;MQ0=1;MQRankSum=-1.230;PG=0,0,0;QD=0.92;ReadPosRankSum=-2.583 GT:AD:GQ:PL:PP 0/1:46,8:99:396,0,7299:396,0,7299 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testNumRefWithPanel.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testNumRefWithPanel.vcf new file mode 100644 index 00000000000..ca0f2496bb6 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors/expectedCGP_testNumRefWithPanel.vcf @@ -0,0 +1,44 @@ +##fileformat=VCFv4.2 +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/rocCurve/2.3-174/.queue/scatterGather/call.and.assess.NA12878-1-sg/temp_64_of_80/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=120 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null 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 logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub graphOutput=null pair_hmm_implementation=LOGLESS_CACHING keepRG=null minPruning=2 gcpHMM=10 minKmer=11 downsampleRegion=1000 useAllelesTrigger=false useFilteredReadsForAnnotations=false dbsnp=(RodBinding name= source=UNBOUND) comp=[] annotation=[ClippingRankSumTest] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=0.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.05 logRemovedReadsFromContaminationFiltering=null exactcallslog=null debug=false activeRegionOut=null activeRegionIn=null filter_mismatching_base_and_quals=false" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[20:10000000-15000000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null 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 logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/rocCurve/chr20.5mb.NA12878.2.3-174.hc.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false regenotype=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_mismatching_base_and_quals=false" +##contig= +##contig= +##reference=human_g1k_v37.fasta +##source=SelectVariants +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +20 10001436 . A AAGGCT 3862.77 . AC=2;AF=1.00;AN=2;DP=48;FS=0.000;HaplotypeScore=9.1318;MLEAC=2;MLEAF=1.00;MQ=42.54;MQ0=0;PG=11,3,0;QD=16.09 GT:AD:GQ:PL:PP 1/1:0,43:99:3891,154,0:3902,157,0 +20 10002458 . G GTTT,GT 756.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=51;FS=0.000;HaplotypeScore=46.1412;MLEAC=1,1;MLEAF=0.500,0.500;MQ=52.11;MQ0=0;PG=0,34,71,34,71,71;QD=7.41 GT:AD:GQ:PL:PP 1/2:0,20,6:99:3411,302,122,899,0,719:3340,265,122,862,0,719 +20 10004223 . A AG 1611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;ClippingRankSum=-2.330;DP=66;FS=0.000;HaplotypeScore=85.7780;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=0;MQRankSum=3.605;PG=0,13,31;QD=24.42;ReadPosRankSum=2.345 GT:AD:GQ:PL:PP 0/1:31,28:99:1640,0,1329:1627,0,1348 +20 10004769 . TAAAACTATGC T 3929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.015;ClippingRankSum=-0.803;DP=79;FS=6.987;HaplotypeScore=16.2718;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-5.938;PG=0,5,15;QD=4.97;ReadPosRankSum=3.465 GT:AD:GQ:PL:PP 0/1:46,26:99:3958,0,5569:3953,0,5580 +20 10006819 . AAAAC A 3457.77 . AC=2;AF=1.00;AN=2;DP=77;FS=0.000;HaplotypeScore=22.5175;MLEAC=2;MLEAF=1.00;MQ=60.82;MQ0=0;PG=11,3,0;QD=11.23 GT:AD:GQ:PL:PP 1/1:0,59:99:3486,178,0:3497,181,0 +20 10008029 . T TA 2579.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.933;ClippingRankSum=0.500;DP=89;FS=0.000;HaplotypeScore=21.5461;MLEAC=2;MLEAF=1.00;MQ=60.92;MQ0=0;MQRankSum=0.122;PG=9,2,0;QD=28.99;ReadPosRankSum=-1.068 GT:AD:GQ:PL:PP 1/1:3,72:99:2608,223,0:2617,225,0 +20 10008146 . TA T 10964.77 . AC=2;AF=1.00;AN=2;DP=74;FS=0.000;HaplotypeScore=24.1439;MLEAC=2;MLEAF=1.00;MQ=60.27;MQ0=0;PG=13,3,0;QD=148.17 GT:AD:GQ:PL:PP 1/1:0,70:99:10993,805,0:11006,808,0 +20 10008758 . C CA 1819.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.813;ClippingRankSum=-1.164;DP=51;FS=4.935;HaplotypeScore=90.2830;MLEAC=2;MLEAF=1.00;MQ=33.83;MQ0=1;MQRankSum=-0.286;PG=3,0,3;QD=35.68;ReadPosRankSum=-0.505 GT:AD:GQ:PL:PP 1/1:4,37:99:1848,126,0:1848,123,0 +20 10008950 . AACACACACACAC A,AACACACACAC 2650.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.622;ClippingRankSum=-0.403;DP=58;FS=0.000;HaplotypeScore=137.9823;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.36;MQ0=0;MQRankSum=0.549;PG=0,34,71,34,71,71;QD=6.53;ReadPosRankSum=0.195 GT:AD:GQ:PL:PP 1/2:2,15,17:99:3592,904,2216,1963,0,1831:3521,867,2216,1926,0,1831 +20 10009882 . GAGAAGAA G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.105;ClippingRankSum=3.616;DP=57;FS=3.656;HaplotypeScore=75.0802;MLEAC=1;MLEAF=0.500;MQ=51.53;MQ0=1;MQRankSum=-1.230;PG=0,34,71;QD=0.92;ReadPosRankSum=-2.583 GT:AD:GQ:PL:PP 0/1:46,8:99:396,0,7299:362,0,7336