zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

When genotyping given alleles, for multiallelic sites we go back to the reads and use the alternate base with the highest sum of quality scores instead of taking the first alternate allele from the vcf file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5701 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-27 21:31:09 +00:00
parent 6e9e766a71
commit 3907377f37
1 changed files with 4 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -81,10 +81,11 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
return null;
}
if ( !vcInput.isBiallelic() ) {
logger.info("Record at position " + ref.getLocus() + " is not bi-allelic; choosing the first allele...");
//return null;
// for multi-allelic sites go back to the reads and find the most likely alternate allele
initializeBestAlternateAllele(refBase, contexts);
} else {
bestAlternateAllele = vcInput.getAlternateAllele(0).getBases()[0];
}
bestAlternateAllele = vcInput.getAlternateAllele(0).getBases()[0];
} else {
initializeBestAlternateAllele(refBase, contexts);
}