Added a multisample concordance walker which takes the place of the VCF python library I've been using. Takes a truth VCF and a variant VCF and outputs A TSV that looks like this:
Sample_ID Concordant_Refs Concordant_Vars Homs_called_het Het_called_homs False_Positives False_Negatives_Due_To_Ref_Call False_Negatives_Due_To_No_Call NA19381 491 294 2 0 0 0 1 NA19451 489 298 1 0 0 0 0 NA19463 486 289 2 3 1 4 3 NA19376 488 296 1 0 2 0 1 NA19317 489 284 5 3 3 3 1 This walker will be merged with GenotypeConcordance once it's clear how to do so. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2715 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
parent
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package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
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import java.util.Arrays;
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import java.util.HashSet;
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import java.util.Set;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Jan 27, 2010
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* Time: 5:48:36 PM
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* To change this template use File | Settings | File Templates.
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*/
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class LocusConcordanceInfo {
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public enum ConcordanceType {
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TRUTH_SET,VARIANT_SET,BOTH_SETS
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}
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private ConcordanceType concordanceType;
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private VCFRecord variantVCFRecord;
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private VCFRecord truthVCFRecord;
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private ReferenceContext reference;
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public LocusConcordanceInfo(ConcordanceType type, VCFRecord truthRecord, VCFRecord variantRecord, ReferenceContext ref) {
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concordanceType = type;
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variantVCFRecord = variantRecord;
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truthVCFRecord = truthRecord;
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reference = ref;
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}
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public boolean concordanceIsCheckable() {
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return concordanceType == ConcordanceType.BOTH_SETS;
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}
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public VCFGenotypeRecord getTruthGenotype(String sample) {
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return truthVCFRecord.getGenotype(sample);
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}
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public VCFGenotypeRecord getVariantGenotype(String sample) {
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return variantVCFRecord.getGenotype(sample);
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}
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public Set<String> getOverlappingSamples() {
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Set<String> variantSamples = new HashSet<String>( Arrays.asList(variantVCFRecord.getSampleNames()) );
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variantSamples.retainAll(Arrays.asList(truthVCFRecord.getSampleNames()));
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return variantSamples;
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}
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public byte getReferenceBase() {
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return (byte) reference.getBase();
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}
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public boolean isTruthOnly () {
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return concordanceType == ConcordanceType.TRUTH_SET;
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}
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public boolean isVariantSite() {
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for ( VCFGenotypeRecord g : truthVCFRecord.getVCFGenotypeRecords() ) {
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if ( g.isVariant(reference.getBase()) ) {
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return true;
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}
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}
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return false;
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}
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public GenomeLoc getLoc() {
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if ( concordanceType == ConcordanceType.TRUTH_SET || concordanceType == ConcordanceType.BOTH_SETS) {
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return truthVCFRecord.getLocation();
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} else {
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return variantVCFRecord.getLocation();
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}
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}
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}
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package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample;
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import java.util.HashSet;
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import java.util.Set;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Jan 27, 2010
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* Time: 5:47:27 PM
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* To change this template use File | Settings | File Templates.
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*/
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class MultiSampleConcordanceSet {
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private HashSet<VCFConcordanceCalculator> concordanceSet;
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private Set<String> cachedSampleNames;
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private long truthOnlySites;
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private long truthOnlyVariantSites;
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private long variantOnlySites;
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private long overlappingSites;
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public MultiSampleConcordanceSet() {
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concordanceSet = new HashSet<VCFConcordanceCalculator>();
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truthOnlySites = 0l;
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truthOnlyVariantSites = 0l;
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variantOnlySites = 0l;
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overlappingSites = 0l;
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}
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public boolean hasBeenInstantiated() {
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return cachedSampleNames != null;
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}
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public void instantiate(Set<String> samples) {
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cachedSampleNames = samples;
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for ( String s : samples ) {
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concordanceSet.add(new VCFConcordanceCalculator(s));
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}
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}
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public void update(LocusConcordanceInfo info) {
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if ( info.concordanceIsCheckable() ) {
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overlappingSites++;
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for ( VCFConcordanceCalculator concordance : concordanceSet ) {
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concordance.update(info);
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}
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} else if ( info.isTruthOnly() ) {
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truthOnlySites++;
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if ( info.isVariantSite() ) {
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truthOnlyVariantSites++;
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}
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} else {
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variantOnlySites++;
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}
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}
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public Set<VCFConcordanceCalculator> getConcordanceSet() {
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return concordanceSet;
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}
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public long numberOfTruthOnlySites() {
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return truthOnlySites;
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}
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public long numberOfTruthOnlyVariantSites() {
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return truthOnlyVariantSites;
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}
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public long numberOfVariantOnlySites() {
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return variantOnlySites;
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}
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public long numberOfOverlappingSites() {
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return overlappingSites;
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}
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}
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package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.RodVCF;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.RMD;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Jan 27, 2010
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* Time: 10:40:44 AM
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* To change this template use File | Settings | File Templates.
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*/
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/*
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* Calculates per-sample concordance metrics across two multi-sample VCF files; outputs simple counts of concordant
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* variant and genotype calls, genotyping errors, and call errors. Requires a VCF binding with the name 'truth' and
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* a VCF binding with the name 'variants'.
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* @Author: Chris Hartl
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*/
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@Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="truth",type= RodVCF.class),@RMD(name="variants",type= RodVCF.class)})
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public class MultiSampleConcordanceWalker extends RodWalker< LocusConcordanceInfo, MultiSampleConcordanceSet > {
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public void initialize() {
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}
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public MultiSampleConcordanceSet reduceInit() {
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return new MultiSampleConcordanceSet();
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}
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public LocusConcordanceInfo map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext c) {
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if ( tracker == null ) {
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return null;
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}
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ReferenceOrderedDatum truthData = tracker.lookup("truth", null);
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ReferenceOrderedDatum variantData = tracker.lookup("variants",null);
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LocusConcordanceInfo concordance;
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if ( truthData == null && variantData == null) {
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concordance = null;
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} else if ( truthData == null ) {
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// not in the truth set
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if ( ( (RodVCF) variantData ).isFiltered() ) {
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concordance = null;
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} else {
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concordance = new LocusConcordanceInfo(LocusConcordanceInfo.ConcordanceType.VARIANT_SET,null, ( (RodVCF) variantData ).getRecord(),ref);
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}
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} else if ( variantData == null ) {
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// not in the variant set
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if ( ( (RodVCF) truthData).isFiltered() ) {
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concordance = null;
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} else {
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concordance = new LocusConcordanceInfo(LocusConcordanceInfo.ConcordanceType.TRUTH_SET,( (RodVCF) truthData).getRecord(),null,ref);
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}
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} else {
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// in both
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// check for filtering
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boolean truth_filter = ((RodVCF) truthData).isFiltered();
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boolean call_filter = ((RodVCF) variantData).isFiltered();
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if ( truth_filter && call_filter ) {
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concordance = null;
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} else if ( truth_filter ) {
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concordance = new LocusConcordanceInfo(LocusConcordanceInfo.ConcordanceType.VARIANT_SET,null, ( (RodVCF) variantData ).getRecord(),ref);
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} else if ( call_filter ) {
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concordance = new LocusConcordanceInfo(LocusConcordanceInfo.ConcordanceType.TRUTH_SET,( (RodVCF) truthData).getRecord(),null,ref);
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} else {
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concordance = new LocusConcordanceInfo(LocusConcordanceInfo.ConcordanceType.BOTH_SETS,( (RodVCF) truthData).getRecord(),( (RodVCF) variantData).getRecord(),ref);
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}
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}
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return concordance;
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}
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public MultiSampleConcordanceSet reduce(LocusConcordanceInfo info, MultiSampleConcordanceSet concordanceSet) {
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if ( info != null ) {
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if ( concordanceSet.hasBeenInstantiated() ) {
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concordanceSet.update(info);
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} else if ( info.concordanceIsCheckable() ) {
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concordanceSet.instantiate(info.getOverlappingSamples());
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concordanceSet.update(info);
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} else {
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concordanceSet.update(info);
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}
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}
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return concordanceSet;
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}
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public void onTraversalDone(MultiSampleConcordanceSet cSet) {
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String[] header = {"Sample_ID","Concordant_Refs","Concordant_Vars","Homs_called_het","Het_called_homs","False_Positives","False_Negatives_Due_To_Ref_Call","False_Negatives_Due_To_No_Call"};
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out.print(String.format("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s%n",header));
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for ( VCFConcordanceCalculator sample : cSet.getConcordanceSet() ) {
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out.print(String.format("%s%n",sample));
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}
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logger.info("Overlapping="+cSet.numberOfOverlappingSites()+"\tTruthOnly="+cSet.numberOfTruthOnlySites()+"\tTruthOnlyVariantSites="+
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cSet.numberOfTruthOnlyVariantSites()+"\tVariantOnly="+cSet.numberOfVariantOnlySites());
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}
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}
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package org.broadinstitute.sting.playground.gatk.walkers.varianteval.multisample;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
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import java.util.HashSet;
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import java.util.Set;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Jan 27, 2010
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* Time: 5:48:08 PM
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* To change this template use File | Settings | File Templates.
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*/
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class VCFConcordanceCalculator {
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private String name;
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private Set<GenomeLoc> falsePositiveLoci;
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private Set<GenomeLoc> falseNegativeLoci;
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private Set<GenomeLoc> falseNegativeLociDueToNoCall;
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private Set<GenomeLoc> hetsCalledHoms;
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private Set<GenomeLoc> homsCalledHets;
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private Set<GenomeLoc> concordantCalls;
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private Set<GenomeLoc> concordantGenotypeReferenceCalls;
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private Set<GenomeLoc> chipNoCalls;
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public VCFConcordanceCalculator(String sampleName) {
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name = sampleName;
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falseNegativeLoci = new HashSet<GenomeLoc>();
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falseNegativeLociDueToNoCall = new HashSet<GenomeLoc>();
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falsePositiveLoci = new HashSet<GenomeLoc>();
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hetsCalledHoms = new HashSet<GenomeLoc>();
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homsCalledHets = new HashSet<GenomeLoc>();
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concordantCalls = new HashSet<GenomeLoc>();
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concordantGenotypeReferenceCalls = new HashSet<GenomeLoc>();
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chipNoCalls = new HashSet<GenomeLoc>();
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}
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public void update(LocusConcordanceInfo info) {
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compareGenotypes(info.getTruthGenotype(name), info.getVariantGenotype(name), info.getLoc(), info.getReferenceBase() );
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}
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public String toString() {
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return String.format("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d",name,concordantGenotypeReferenceCalls.size(),concordantCalls.size(),homsCalledHets.size(),hetsCalledHoms.size(),falsePositiveLoci.size(),falseNegativeLoci.size(),falseNegativeLociDueToNoCall.size());
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}
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private void compareGenotypes(VCFGenotypeRecord truth, VCFGenotypeRecord call, GenomeLoc loc, byte ref) {
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if ( truth.isNoCall() ) {
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chipNoCalls.add(loc);
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} else if ( truth.isVariant(( char) ref) ) {
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if ( call.isNoCall() ) {
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falseNegativeLociDueToNoCall.add(loc);
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} else if ( ! call.isVariant( (char) ref ) ) {
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falseNegativeLoci.add(loc);
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} else if ( call.isVariant((char) ref) ) {
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// check het vs hom
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checkGenotypeCall(truth,call, loc);
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}
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} else if ( ! truth.isVariant( (char) ref ) ) {
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if ( call.isVariant((char) ref) ) {
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falsePositiveLoci.add(loc);
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} else {
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concordantGenotypeReferenceCalls.add(loc);
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}
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}
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}
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private void checkGenotypeCall( VCFGenotypeRecord truth, VCFGenotypeRecord call, GenomeLoc loc ) {
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if ( truth.isHet() && call.isHom() ) {
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hetsCalledHoms.add(loc);
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} else if ( truth.isHom() && call.isHet() ) {
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homsCalledHets.add(loc);
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} else if ( ( truth.isHet() && call.isHet() ) || ( truth.isHom() && call.isHom() ) ) { // be extra careful
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concordantCalls.add(loc);
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}
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}
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}
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