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Don't skip tri-allelic alleles passed in - just choose the first one. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5293 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-23 17:25:50 +00:00
parent a2301383bb
commit 9357bee921
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -73,14 +73,14 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true); final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
if ( vcInput == null ) if ( vcInput == null )
return null; return null;
if ( !vcInput.isBiallelic() ) {
logger.info("Record at position " + ref.getLocus() + " is not bi-allelic; skipping...");
return null;
}
if ( !vcInput.isSNP() ) { if ( !vcInput.isSNP() ) {
logger.info("Record at position " + ref.getLocus() + " is not a SNP; skipping..."); logger.info("Record at position " + ref.getLocus() + " is not a SNP; skipping...");
return null; return null;
} }
if ( !vcInput.isBiallelic() ) {
logger.info("Record at position " + ref.getLocus() + " is not bi-allelic; choosing the first allele...");
//return null;
}
bestAlternateAllele = vcInput.getAlternateAllele(0).getBases()[0]; bestAlternateAllele = vcInput.getAlternateAllele(0).getBases()[0];
} else { } else {
initializeBestAlternateAllele(refBase, contexts); initializeBestAlternateAllele(refBase, contexts);