From ed4cf3de576269b028e753c332f805506ed91f6d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 Nov 2009 20:20:48 +0000
Subject: [PATCH] Check that we're biallelic before calling isSNP()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2127 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/SNPClusterWalker.java             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java
index d8502b416..997edb00b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java
@@ -23,7 +23,7 @@ public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
 
     public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         Variation snp = (Variation)tracker.lookup("snps", null);
-        return (snp != null && snp.isSNP()) ? context.getLocation() : null;
+        return (snp != null && snp.isBiallelic() && snp.isSNP()) ? context.getLocation() : null;
     }
 
     public void onTraversalDone(GenomeLoc sum) {