diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java
index 8eb53b5bc..88b0f0651 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java
@@ -32,6 +32,8 @@ public class VECFisherStrand implements VariantExclusionCriterion {
 
     public static boolean strandTest(char ref, LocusContext context, int allele1, int allele2, double threshold, StringBuffer out) {
         int[][] table = getContingencyTable(context, allele1, allele2);
+        if ( !variantIsHet(table) )
+            return false;
 
         double pCutoff = computePValue(table);
         //printTable(table, pCutoff);
@@ -75,6 +77,10 @@ public class VECFisherStrand implements VariantExclusionCriterion {
         return pValue < threshold;
     }
 
+    private static boolean variantIsHet(int[][] table) {
+        return ((table[0][1] != 0 || table[0][1] != 0) && (table[1][0] != 0 || table[1][1] != 0));
+    }
+
     private void printTable(int[][] table, double pValue) {
         System.out.printf("%d %d; %d %d : %f\n", table[0][0], table[0][1], table[1][0], table[1][1], pValue);
     }