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Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3521 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-06-09 18:05:37 +00:00
parent fdded73861
commit 20167fd411
1 changed files with 32 additions and 34 deletions
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56
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
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@ -62,34 +62,13 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
homozygousRegions.put(dad,null); homozygousRegions.put(dad,null);
homozygousRegionCounts.put(child,0); homozygousRegionCounts.put(child,0);
homozygousRegionCounts.put(mom,0); homozygousRegionCounts.put(mom,0);
homozygousRegionCounts.put(dad,0);
regionKeys = new HashMap<String,MendelianInfoKey>(3); regionKeys = new HashMap<String,MendelianInfoKey>(3);
regionKeys.put(child,MendelianInfoKey.ChildHomozygosityRegion); regionKeys.put(child,MendelianInfoKey.ChildHomozygosityRegion);
regionKeys.put(mom,MendelianInfoKey.MotherHomozygosityRegion); regionKeys.put(mom,MendelianInfoKey.MotherHomozygosityRegion);
regionKeys.put(dad,MendelianInfoKey.FatherHomozygosityRegion); regionKeys.put(dad,MendelianInfoKey.FatherHomozygosityRegion);
} }
public void updateHomozygosityRegions(Map<String,Genotype> genotypes, GenomeLoc loc) {
for ( Map.Entry<String,Genotype> memberGenotype : genotypes.entrySet() ) {
if ( homozygousRegions.get(memberGenotype.getKey()) == null ) {
// currently in a heterozygous region, update if possible
if ( memberGenotype.getValue().isHom() ) {
homozygousRegionCounts.put(memberGenotype.getKey(),homozygousRegionCounts.get(memberGenotype.getKey())+1);
homozygousRegions.put(memberGenotype.getKey(),new HomozygosityRegion(loc));
}
} else {
// potentially breaking a homozygous region
if ( memberGenotype.getValue().isHom() ) {
// no break, continuing
homozygousRegions.get(memberGenotype.getKey()).callsWithinRegion++;
} else {
// break of homozygosity, reset region to null, print to file, do not update the count yet
homozygousRegions.put(memberGenotype.getKey(),null);
}
}
}
}
public void updateHomozygosityRegions(MendelianViolation v, PrintStream output) { public void updateHomozygosityRegions(MendelianViolation v, PrintStream output) {
if ( ! v.siteIsFiltered() ) { if ( ! v.siteIsFiltered() ) {
ArrayList<HomozygosityRegion> brokenRegions = new ArrayList<HomozygosityRegion>(3); ArrayList<HomozygosityRegion> brokenRegions = new ArrayList<HomozygosityRegion>(3);
@ -329,6 +308,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
uac.STANDARD_CONFIDENCE_FOR_CALLING = 30; uac.STANDARD_CONFIDENCE_FOR_CALLING = 30;
engine = new UnifiedGenotyperEngine(getToolkit(),uac); engine = new UnifiedGenotyperEngine(getToolkit(),uac);
logger.info("Mom: "+trioStructure.mom+" Dad: "+trioStructure.dad+" Child: "+trioStructure.child); logger.info("Mom: "+trioStructure.mom+" Dad: "+trioStructure.dad+" Child: "+trioStructure.child);
bedOutput.printf("%s%n",getBedFileHeader());
} }
/* /*
@ -348,21 +328,34 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
return writer; return writer;
} }
/*
***************** FILTER
*/
public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
return tracker != null;
}
/* /*
*************** MAP *************** MAP
*/ */
public MendelianViolation map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public MendelianViolation map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) { return assessViolation(tracker.getVariantContext(ref,"trio", EnumSet.of(VariantContext.Type.SNP),ref.getLocus(),true),tracker,ref,context);
return null;
} }
return assessViolation(tracker.getVariantContext(ref,"trio", EnumSet.of(VariantContext.Type.SNP),ref.getLocus(),true),tracker,ref,context); private boolean isComplete(VariantContext vc) {
for ( Genotype g : vc.getGenotypes().values() ) {
if ( g.isNoCall() || g.isFiltered() ) {
return false;
}
}
return true;
} }
private MendelianViolation assessViolation(VariantContext varContext, RefMetaDataTracker tracker, ReferenceContext reference, AlignmentContext context) { private MendelianViolation assessViolation(VariantContext varContext, RefMetaDataTracker tracker, ReferenceContext reference, AlignmentContext context) {
MendelianViolation violation; MendelianViolation violation;
if ( varContext != null ) { if ( varContext != null ) {
if ( MendelianViolationEvaluator.isViolation(varContext,trioStructure) ) { if ( isComplete(varContext) && MendelianViolationEvaluator.isViolation(varContext,trioStructure) ) {
if ( isDeNovo(varContext) ) { if ( isDeNovo(varContext) ) {
violation = assessDeNovo(varContext,tracker,reference,context); violation = assessDeNovo(varContext,tracker,reference,context);
} else if ( isOppositeHomozygote(varContext) ) { } else if ( isOppositeHomozygote(varContext) ) {
@ -410,9 +403,14 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
if ( ! trio.isFiltered() ) { if ( ! trio.isFiltered() ) {
Allele parental = trio.getGenotype(trioStructure.mom).getAllele(0); // guaranteed homozygous Allele parental = trio.getGenotype(trioStructure.mom).getAllele(0); // guaranteed homozygous
if ( parental.getBases().length < 1 ) {
throw new StingException("Parental bases have length zero at "+trio.toString());
}
int numParental = 0; int numParental = 0;
int total = 0; int total = 0;
for ( PileupElement e : StratifiedAlignmentContext.splitContextBySample(context.getBasePileup()).get(trioStructure.child).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup() ) { StratifiedAlignmentContext childCon = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup()).get(trioStructure.child);
if ( childCon != null ) {
for ( PileupElement e : childCon.getPileupElements(StratifiedAlignmentContext.StratifiedContextType.COMPLETE) ) {
if ( e.getQual() >= 10 && e.getMappingQual() >= 10 ) { if ( e.getQual() >= 10 && e.getMappingQual() >= 10 ) {
total++; total++;
if ( e.getBase() == parental.getBases()[0] ) { if ( e.getBase() == parental.getBases()[0] ) {
@ -422,7 +420,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
} }
violation.addAttribute(MendelianInfoKey.ProportionOfParentAllele.getKey(), ((double) numParental)/total); violation.addAttribute(MendelianInfoKey.ProportionOfParentAllele.getKey(), ((double) numParental)/total);
} }
}
return violation; return violation;
} }
@ -439,7 +437,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
Allele alt = null; Allele alt = null;
for ( Map.Entry<String,StratifiedAlignmentContext> stratifiedEntry : stratCon.entrySet() ) { for ( Map.Entry<String,StratifiedAlignmentContext> stratifiedEntry : stratCon.entrySet() ) {
VariantCallContext call = engine.runGenotyper(tracker,ref,stratifiedEntry.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE)); VariantCallContext call = engine.runGenotyper(tracker,ref,stratifiedEntry.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE));
if ( call != null && call.confidentlyCalled ) { if ( call != null && call.confidentlyCalled && call.vc != null) {
if ( call.vc.isSNP() ) { if ( call.vc.isSNP() ) {
if ( ! call.vc.getAlternateAllele(0).basesMatch(trio.getAlternateAllele(0)) ) { if ( ! call.vc.getAlternateAllele(0).basesMatch(trio.getAlternateAllele(0)) ) {
if ( alt == null ) { if ( alt == null ) {