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Two changes to HC GGA mode to make it more like the UG. 

-- Only try to genotype PASSing records in the alleles file
-- Don't attempt to genotype multiple records with the same start location. Instead take the first record and throw a warning message.
This commit is contained in:
Ryan Poplin 2013-04-01 10:20:04 -04:00
parent 7c83efc1b9
commit f65206e758
1 changed files with 3 additions and 6 deletions
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9
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -451,12 +451,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
public ActivityProfileState isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) {
if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
for( final VariantContext vc : tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()) ) {
if( !allelesToGenotype.contains(vc) ) {
allelesToGenotype.add(vc); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object
}
}
if( tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ) {
final VariantContext vcFromAllelesRod = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, ref.getLocus(), false, logger, UG_engine.getUAC().alleles);
if( vcFromAllelesRod != null ) {
allelesToGenotype.add(vcFromAllelesRod); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object
return new ActivityProfileState(ref.getLocus(), 1.0);
}
}