From 3907377f3724bdadc580a024e3ea671d15e92e7e Mon Sep 17 00:00:00 2001 From: rpoplin Date: Wed, 27 Apr 2011 21:31:09 +0000 Subject: [PATCH] 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 --- .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index f57c8873e..54ce35bbd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -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); }