From e64d1be475f0acd8efdc62a5299411de2fd22923 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 30 Aug 2010 20:43:37 +0000
Subject: [PATCH] Check if VC is null before trying to subset it (can happen
 with indels)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4165 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/SelectVariants.java        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 10c5293a6..942d81bf4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -203,6 +203,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
             return 0;
 
         VariantContext vc = tracker.getVariantContext(ref, "variant", null, context.getLocation(), true);
+	if ( vc == null ){
+	    return 0;
+	}
         VariantContext sub = subsetRecord(vc, samples);
 
         if ( (sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {