From 5a8e2c273929cf2fea221da23704917743de7b39 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Wed, 2 Feb 2011 15:12:26 +0000 Subject: [PATCH] Going through the backlog of emergency hacks I put in for the 1000G release. It is possible to call a site in an analysis panel but when using all samples the site isn't called because of going over the minimum deletion threshold, for example. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5174 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/genotyper/UGCalcLikelihoods.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java index e2460962c..d9f6a3420 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java @@ -111,7 +111,7 @@ public class UGCalcLikelihoods extends LocusWalker } public Integer reduce(VariantCallContext value, Integer sum) { - if ( value == null ) + if ( value == null || value.vc == null ) return sum; try {