diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
index da3ed2a02..b0452f9ea 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
@@ -627,7 +627,10 @@ public class GeneralPloidyExactAFCalculation extends ExactAFCalculation {
             // create the new likelihoods array from the alleles we are allowed to use
             final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
             double[] newLikelihoods;
-            if ( numOriginalAltAlleles == numNewAltAlleles) {
+
+            // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
+            // and subsetting
+            if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
                 newLikelihoods = originalLikelihoods;
             } else {
                 newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);