-UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one)
-MQ0 annotation is now standard again -Added AC and AN annotations to VCF output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2545 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
f587ff46af
commit
b468369dfa
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@ -44,7 +44,7 @@ public class StratifiedAlignmentContext {
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// Definitions:
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// COMPLETE = full alignment context
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// FORWARD = reads on forward strand
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// FORWARD = reads on forward strand
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// REVERSE = reads on forward strand
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//
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public enum StratifiedContextType { COMPLETE, FORWARD, REVERSE }
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@ -82,6 +82,18 @@ public class StratifiedAlignmentContext {
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offsets[StratifiedContextType.COMPLETE.ordinal()].add(offset);
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}
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/**
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* Splits the given AlignmentContext into a StratifiedAlignmentContext per sample.
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*
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* @param pileup the original pileup
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*
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* @return a Map of sample name to StratifiedAlignmentContext
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*
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**/
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public static Map<String, StratifiedAlignmentContext> splitContextBySample(ReadBackedPileup pileup) {
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return splitContextBySample(pileup, null, null);
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}
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/**
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* Splits the given AlignmentContext into a StratifiedAlignmentContext per sample.
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*
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@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
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import java.util.Map;
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public class MappingQualityZero implements VariantAnnotation {
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public class MappingQualityZero extends StandardVariantAnnotation {
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public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
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int mq0 = 0;
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@ -166,7 +166,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 &&
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variant.isBiallelic() &&
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variant.isSNP() ) {
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Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup(), null, null);
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Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
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if ( stratifiedContexts != null )
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annotations = getAnnotations(tracker, ref, stratifiedContexts, variant, requestedAnnotations);
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}
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@ -75,9 +75,15 @@ public class UnifiedArgumentCollection {
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@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
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public int MIN_BASE_QUALTY_SCORE = 20;
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@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
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public int MIN_MAPPING_QUALTY_SCORE = 10;
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@Argument(fullName = "max_mismatches_in_40bp_window", shortName = "mm40", doc = "Maximum number of mismatches within a 40 bp window (20bp on either side) around the target position for a read to be used for calling", required = false)
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public int MAX_MISMATCHES = 3;
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@Argument(fullName = "use_reads_with_bad_mates", shortName = "bad_mates", doc = "Use reads whose mates are mapped excessively far away for calling", required = false)
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public boolean USE_BADLY_MATED_READS = false;
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@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
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public Double MAX_DELETION_FRACTION = 0.05;
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@ -26,7 +26,6 @@
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package org.broadinstitute.sting.gatk.walkers.genotyper;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.filters.*;
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import org.broadinstitute.sting.gatk.contexts.*;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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@ -49,7 +48,6 @@ import java.io.FileNotFoundException;
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* multi-sample, and pooled data. The user can choose from several different incorporated calculation models.
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*/
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@Reference(window=@Window(start=-20,stop=20))
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@ReadFilters({ZeroMappingQualityReadFilter.class,MappingQualityReadFilter.class,BadMateReadFilter.class})
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public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genotype>>, Integer> implements TreeReducible<Integer> {
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@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
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@ -178,15 +176,16 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
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headerInfo.addAll(VariantAnnotator.getVCFAnnotationDescriptions());
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// annotation (INFO) fields from UnifiedGenotyper
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headerInfo.add(new VCFHeaderLine("INFO_NOTE", "\"All annotations in the INFO field are generated only from the FILTERED context used for calling variants\""));
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headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_FREQUENCY_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));
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// no longer used: headerInfo.add(new VCFInfoHeaderLine(VCFRecord.SAMPLE_NUMBER_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Number of Samples With Data"));
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if ( !UAC.NO_SLOD )
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headerInfo.add(new VCFInfoHeaderLine(VCFRecord.STRAND_BIAS_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Strand Bias"));
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// FORMAT fields if not in POOLED mode
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if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED )
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if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED ) {
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headerInfo.addAll(VCFGenotypeRecord.getSupportedHeaderStrings());
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headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_COUNT_KEY, 2, VCFInfoHeaderLine.INFO_TYPE.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
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headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_NUMBER_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Total number of alleles in called genotypes"));
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}
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// all of the arguments from the argument collection
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Set<Object> args = new HashSet<Object>();
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@ -229,10 +228,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
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return null;
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// filter the context based on min base and mapping qualities
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ReadBackedPileup pileup = rawContext.getPileup().getBaseFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
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ReadBackedPileup pileup = rawContext.getBasePileup().getBaseFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
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// filter the context based on mismatches
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pileup = filterPileup(pileup, refContext, UAC.MAX_MISMATCHES);
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// filter the context based on mapping quality and mismatch rate
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pileup = filterPileup(pileup, refContext, UAC);
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// an optimization to speed things up when there is no coverage or when overly covered
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if ( pileup.size() == 0 ||
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@ -255,6 +254,9 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
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// annotate the call, if possible
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if ( call != null && call.first != null && call.first instanceof ArbitraryFieldsBacked ) {
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// first off, we want to use the *unfiltered* context for the annotations
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stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup());
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Map<String, String> annotations;
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if ( UAC.ALL_ANNOTATIONS )
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annotations = VariantAnnotator.getAllAnnotations(tracker, refContext, stratifiedContexts, call.first);
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@ -267,14 +269,16 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
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}
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// filter based on maximum mismatches and bad mates
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private static ReadBackedPileup filterPileup(ReadBackedPileup pileup, ReferenceContext refContext, int maxMismatches) {
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private static ReadBackedPileup filterPileup(ReadBackedPileup pileup, ReferenceContext refContext, UnifiedArgumentCollection UAC) {
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ArrayList<PileupElement> filteredPileup = new ArrayList<PileupElement>();
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for ( PileupElement p : pileup ) {
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if ( AlignmentUtils.mismatchesInRefWindow(p, refContext, true) <= maxMismatches )
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if ( p.getMappingQual() >= UAC.MIN_MAPPING_QUALTY_SCORE &&
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(UAC.USE_BADLY_MATED_READS || !p.getRead().getReadPairedFlag() || p.getRead().getMateUnmappedFlag() || p.getRead().getMateReferenceIndex() == p.getRead().getReferenceIndex()) &&
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AlignmentUtils.mismatchesInRefWindow(p, refContext, true) <= UAC.MAX_MISMATCHES )
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filteredPileup.add(p);
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}
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return new ReadBackedPileup(pileup.getLocation(), filteredPileup);
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}
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private static boolean isValidDeletionFraction(double d) {
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@ -112,11 +112,13 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
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Map<String, VCFGenotypeCall> genotypeMap = genotypeListToSampleNameMap(genotypes);
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int totalAlleles = 0;
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for (String name : mHeader.getGenotypeSamples()) {
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if (genotypeMap.containsKey(name)) {
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Genotype gtype = genotypeMap.get(name);
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VCFGenotypeRecord record = VCFUtils.createVCFGenotypeRecord(params, (VCFGenotypeCall)gtype);
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params.addGenotypeRecord(record);
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totalAlleles += record.getAlleles().size();
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genotypeMap.remove(name);
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} else {
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VCFGenotypeRecord record = createNoCallRecord(name);
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@ -132,6 +134,20 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
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// info fields
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Map<String, String> infoFields = getInfoFields((VCFVariationCall)locusdata);
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if ( totalAlleles > 0 ) {
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infoFields.put(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", totalAlleles));
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// the allele counts are a bit trickier - we need to count up the alternate counts to get the ref count
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List<Integer> altAlleleCounts = params.getAlleleCounts();
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int totalAltAlleles = 0;
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StringBuffer sb = new StringBuffer();
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for ( int alleleCount : altAlleleCounts ) {
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sb.append(",");
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sb.append(alleleCount);
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totalAltAlleles += alleleCount;
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}
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infoFields.put(VCFRecord.ALLELE_COUNT_KEY, String.format("%d%s", (totalAlleles - totalAltAlleles), sb.toString()));
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}
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// q-score
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double qual = (locusdata == null) ? 0 : ((VCFVariationCall)locusdata).getConfidence();
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@ -152,7 +168,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
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VCFRecord.UNFILTERED,
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infoFields,
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params.getFormatString(),
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params.getGenotypesRecords());
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params.getGenotypeRecords());
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mWriter.addRecord(vcfRecord, validationStringency);
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}
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@ -180,7 +196,6 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
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infoFields.putAll(otherFields);
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}
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}
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// no longer used: infoFields.put(VCFRecord.SAMPLE_NUMBER_KEY, String.valueOf(params.getGenotypesRecords().size()));
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return infoFields;
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}
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@ -16,9 +16,10 @@ class VCFParameters {
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private int position = 0;
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private String contig = null;
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private boolean initialized = false;
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private List<VCFGenotypeRecord> genotypesRecord = new ArrayList<VCFGenotypeRecord>();
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private List<VCFGenotypeRecord> genotypeRecords = new ArrayList<VCFGenotypeRecord>();
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private List<String> formatList = new ArrayList<String>();
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private List<VCFGenotypeEncoding> alternateBases = new ArrayList<VCFGenotypeEncoding>();
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private List<Integer> alleleCounts = new ArrayList<Integer>();
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public void setLocations(GenomeLoc location, char refBase) {
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// if we haven't set it up, we initialize the object
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@ -56,7 +57,12 @@ class VCFParameters {
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}
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public void addGenotypeRecord(VCFGenotypeRecord record) {
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this.genotypesRecord.add(record);
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genotypeRecords.add(record);
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for ( VCFGenotypeEncoding allele : record.getAlleles() ) {
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int index = alternateBases.indexOf(allele);
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if ( index != -1 ) // we don't keep track of ref alleles here
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alleleCounts.set(index, alleleCounts.get(index)+1);
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}
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}
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public void addFormatItem(String item) {
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@ -67,19 +73,26 @@ class VCFParameters {
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public void addAlternateBase(VCFGenotypeEncoding base) {
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if ( !alternateBases.contains(base) &&
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!base.toString().equals(String.valueOf(getReferenceBase()).toUpperCase()) &&
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!base.toString().equals(VCFGenotypeRecord.EMPTY_ALLELE) )
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!base.toString().equals(VCFGenotypeRecord.EMPTY_ALLELE) ) {
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alternateBases.add(base);
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alleleCounts.add(0);
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}
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}
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public List<VCFGenotypeEncoding> getAlternateBases() {
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return alternateBases;
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}
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// the list of allele counts where each entry relates to the corresponding entry in the Alternate Base list
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public List<Integer> getAlleleCounts() {
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return alleleCounts;
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}
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public String getFormatString() {
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return Utils.join(VCFRecord.FORMAT_FIELD_SEPERATOR, formatList);
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}
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public List<VCFGenotypeRecord> getGenotypesRecords() {
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return genotypesRecord;
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public List<VCFGenotypeRecord> getGenotypeRecords() {
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return genotypeRecords;
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}
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}
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@ -180,7 +180,6 @@ public class VCFUtils {
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Map<String, String> infoFields = new HashMap<String, String>();
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infoFields.put(VCFRecord.DEPTH_KEY, String.format("%d", totalReadDepth));
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// no longer used: infoFields.put(VCFRecord.SAMPLE_NUMBER_KEY, String.valueOf(params.getGenotypesRecords().size()));
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// set the overall strand bias and allele frequency to be the average of all entries we've seen
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if ( SLODsSeen > 0 )
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@ -197,7 +196,7 @@ public class VCFUtils {
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filters.size() == 0 ? "0" : Utils.join(";", filters),
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infoFields,
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params.getFormatString(),
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params.getGenotypesRecords());
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params.getGenotypeRecords());
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}
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/**
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@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("b0012ffce509196885bfdf1612086263"));
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Arrays.asList("ad0d78f399bba23227cf07341708e27d"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("7e00e94a046e82ac41f6fd298a64cc74"));
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Arrays.asList("17119c073a964620809eaaf3a39dfbc4"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("a6630eec84161a089dde204e09744c45"));
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Arrays.asList("b8609ff527e0882dfbe3505357fd2705"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("130658564083f650981b28728b813917"));
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Arrays.asList("e865132880c6aa07bfdd725408fc21e8"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1PointEM() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("8acbb0879a7c9f35e7cf7d77a7cab850"));
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Arrays.asList("706efd396f3ac5e3addff73c15d1ec87"));
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executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
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}
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@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot2PointEM() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("a5ec48e6695d9a5e7fcced7775baf6ff"));
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Arrays.asList("917d9ede2b2bccbcc41c6b7534788fa2"));
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executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
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}
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@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testPooled1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
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Arrays.asList("c20f370440ed55b0b6c38715985a850d"));
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Arrays.asList("48b3719bf39705983876276b8da2642f"));
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executeTest("testPooled1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -56,7 +56,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMultiSamplePilot1Joint() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
|
||||
Arrays.asList("0a2df3fc9fc72a3ace46aab899275636"));
|
||||
Arrays.asList("057493e22a64cf5c78619707464cedbe"));
|
||||
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
|
||||
}
|
||||
|
||||
|
|
@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMultiSamplePilot2Joint() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
|
||||
Arrays.asList("52249b69d5d984a8bdc0438e1f106dcb"));
|
||||
Arrays.asList("05f32f8ba686260b79c98c661a01e8f8"));
|
||||
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
|
||||
}
|
||||
|
||||
|
|
@ -72,7 +72,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testSingleSamplePilot2Joint() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
|
||||
Arrays.asList("172ca88b718f24fa0f2a3460b2dab33d"));
|
||||
Arrays.asList("5fcc0ecff04d408d33ce5fdc0a8d8b89"));
|
||||
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
|
||||
}
|
||||
|
||||
|
|
@ -85,7 +85,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testParallelization() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1,
|
||||
Arrays.asList("d86d9148b1eee16da9a5bb57c929c0c9"));
|
||||
Arrays.asList("b0e221e54f8ff9c6355654510acb7153"));
|
||||
executeTest("test parallelization", spec);
|
||||
}
|
||||
|
||||
|
|
@ -98,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testParameter() {
|
||||
HashMap<String, String> e = new HashMap<String, String>();
|
||||
e.put( "-genotype", "b3161d019d467d5f9045d2f5d7203006" );
|
||||
e.put( "-all_bases", "655c7b8ce2f794a055fa49962b5a6a79" );
|
||||
e.put( "--min_base_quality_score 26", "67175e0262e626d46aaf3bc8680cf888" );
|
||||
e.put( "--min_mapping_quality_score 26", "8edb24206529a7a344008280ab69cbb2" );
|
||||
e.put( "--max_mismatches_in_40bp_window 5", "870812ed23b2c656439dc1c8e6376f89" );
|
||||
e.put( "-genotype", "d82b53aad30005330203a7ca07ce83d5" );
|
||||
e.put( "-all_bases", "563566eaa2c621e88080149512d368b6" );
|
||||
e.put( "--min_base_quality_score 26", "015509aca82954b89d7dc83134f2103e" );
|
||||
e.put( "--min_mapping_quality_score 26", "ba7fe92be077750225c762981ead4b0d" );
|
||||
e.put( "--max_mismatches_in_40bp_window 5", "abecda3de7b195d6d0f7ff97bc624b5f" );
|
||||
|
||||
for ( Map.Entry<String, String> entry : e.entrySet() ) {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
|
|
@ -116,7 +116,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testConfidence() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1,
|
||||
Arrays.asList("eb708a714a0ecbebed707f2d9684e165"));
|
||||
Arrays.asList("c434515cae99d2da5a353f0b0866af81"));
|
||||
executeTest("testConfidence", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue