From ae42c0c7da80a8ad3b31793c8ff7cc150f0c08c3 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Mar 2011 14:18:12 +0000
Subject: [PATCH] Bug fix based on GATK run report

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5354 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 16e5a5702..2e8eea121 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -211,6 +211,8 @@ public class UnifiedGenotyperEngine {
         VariantContext vc;
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
             final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
+            if ( vcInput == null )
+                return null;
             vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
         } else {
             Set<Allele> alleles = new HashSet<Allele>();