From 3db38c5a93d80ede80cb8eb53bb630a1a6ee9490 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Thu, 18 Oct 2012 15:42:14 -0400
Subject: [PATCH] Bug fix: inbreeding coeff shouldn't be computed in ref-only
 sites

---
 .../sting/gatk/walkers/annotator/InbreedingCoeff.java           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index 64be64afa..9a4de3c36 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -48,7 +48,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
 
     private Map<String, Object> calculateIC(final VariantContext vc) {
         final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds);
-        if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
+        if ( genotypes == null || genotypes.size() < MIN_SAMPLES || !vc.isVariant())
             return null;
 
         int idxAA = 0, idxAB = 1, idxBB = 2;