diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index c86a9c357..57e67764c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -236,6 +236,7 @@ public class UnifiedGenotyperEngine {
             clearAFarray(log10AlleleFrequencyPosteriors.get());
             afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get());
             double forwardLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
+            bestAFguess = MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors.get());
             double forwardLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess];
             //System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF);
 
@@ -245,6 +246,7 @@ public class UnifiedGenotyperEngine {
             clearAFarray(log10AlleleFrequencyPosteriors.get());
             afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get());
             double reverseLog10PofNull = log10AlleleFrequencyPosteriors.get()[0];
+            bestAFguess = MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors.get());
             double reverseLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess];
             //System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ", reverseLog10PofF=" + reverseLog10PofF);