From 4a95f2181dee3090375386f4c9af885986aaa62d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 8 Sep 2009 01:37:35 +0000
Subject: [PATCH] print out the right variant

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1543 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/concordance/SNPGenotypeConcordance.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java
index 2c4831155..13da5b6c8 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java
@@ -102,7 +102,7 @@ public class SNPGenotypeConcordance implements ConcordanceType {
         else if ( call1.isSNP() && call2.isReference() && bestVsRef1 >= LOD )
              printVariant(refVsVar1Writer, call1);
         else if ( call2.isSNP() && call1.isReference() && bestVsRef2 >= LOD )
-            printVariant(refVsVar2Writer, call1);
+            printVariant(refVsVar2Writer, call2);
     }
 
     private boolean sameVariantAllele(String genotype1, String genotype2, char ref) {