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We need to allow reference calls in the input VCF for the GenotypeAndValidate walker when using the BAM as truth so that we can test supposed monomorphic calls against the truth.

This commit is contained in:
Eric Banks 2011-08-29 13:19:35 -04:00
parent 5b56c83401
commit bb7a37e8f2
1 changed files with 6 additions and 4 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
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@ -347,12 +347,14 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
}
VariantCallContext call;
if ( vcComp.isSNP() )
if ( vcComp.isSNP() ) {
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
else if ( vcComp.isIndel() ) {
} else if ( vcComp.isIndel() ) {
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
}
else {
} else if ( bamIsTruth ) {
// assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
} else {
logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
return counter;
}