diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java
index 36ea0ae07..2130b623f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java
@@ -267,7 +267,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
         ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
         if ( applyToVariant(variant) ) {
             Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
-            GenotypeFeatureData gfd = dataTable.get(variant.getBestGenotype());
+            GenotypeFeatureData gfd = dataTable.get(orderedBases(variant.getBestGenotype()));
 
             if (integrateOverSamplingProbabilities)
                 exclude = integralExclude(gfd, counts);
@@ -314,4 +314,10 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
         //double value = counts.first / (1.0 * Math.max(counts.second, 1.0));
         return ! gfd.passesThreshold(value);
     }
+
+    private String orderedBases(String s) {
+        char[] charArray = s.toCharArray();
+        java.util.Arrays.sort(charArray);
+        return new String(charArray);
+    }
 }
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