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Bug fixes and enhancements to run whole-genome indel VQSR, removed old chr20-only code and cleanup

This commit is contained in:
Guillermo del Angel 2011-08-02 13:17:20 -04:00
parent a6a87006a5
commit 821bbfa9e0
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -258,7 +258,7 @@ public class VariantDataManager {
datum.consensusCount = 0;
for( final TrainingSet trainingSet : trainingSets ) {
for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) {
for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), true, false ) ) {
if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() &&
((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) &&
(TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {