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Minimal necessary (but most likely not sufficient) changes to run VQSR on indel data: don't fill Ti/Tv fields if non-SNP, request VC only st start of position, check if isSNP() before doing snp-specific operations. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5062 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-01-24 02:36:36 +00:00
parent a51061fd96
commit fd864e8e3a
1 changed files with 6 additions and 4 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -245,7 +245,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
return mapList;
}
final Collection<VariantContext> vcsTruth = tracker.getVariantContexts(ref, truthNames, null, context.getLocation(), false, true);
final Collection<VariantContext> vcsTruth = tracker.getVariantContexts(ref, truthNames, null, context.getLocation(), true, true);
boolean isAtTruthSite = false;
for( final VariantContext vcTruth : vcsTruth ) {
if( vcTruth != null && vcTruth.isVariant() && !vcTruth.isFiltered() && (!vcTruth.hasGenotypes() || vcTruth.isPolymorphic()) ) {
@ -255,12 +255,14 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
}
nTruthSites += isAtTruthSite ? 1 : 0;
for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) {
if( vc != null && vc.isSNP() ) {
for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
if( vc != null ) {
if( !vc.isFiltered() || IGNORE_ALL_INPUT_FILTERS || (ignoreInputFilterSet != null && ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
if( vc.getPhredScaledQual() >= QUAL_THRESHOLD ) {
final VariantDatum variantDatum = new VariantDatum();
variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
if (vc.isSNP())
variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
final Collection<VariantContext> vcsDbsnp = tracker.getVariantContexts(ref, "dbsnp", null, context.getLocation(), false, true);
final Collection<VariantContext> vcsHapMap = tracker.getVariantContexts(ref, "hapmap", null, context.getLocation(), false, true);