diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java
index ab5de65d0..24a1b93f3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java
@@ -41,11 +41,14 @@ public class VECAlleleBalance extends RatioFilter {
      */
     protected Pair<Integer, Integer> getRatioCounts(char ref, ReadBackedPileup pileup, RodGeliText variant) {
         final String genotype = variant.getBestGenotype();
-        final String bases = pileup.getBases();
-
         if ( genotype.length() > 2 )
             throw new IllegalArgumentException(String.format("Can only handle diploid genotypes: %s", genotype));
 
+        final String bases = pileup.getBases();
+        if ( bases.length() == 0 ) {
+            ratio = 0.0;
+            return new Pair<Integer, Integer>(0, 0);
+        }
 
         char a = genotype.toUpperCase().charAt(0);
         char b = genotype.toUpperCase().charAt(1);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java
index df535038e..43a3e89e1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java
@@ -36,13 +36,16 @@ public class VECOnOffGenotypeRatio extends RatioFilter {
     */
     protected Pair<Integer, Integer> getRatioCounts(char ref, ReadBackedPileup pileup, RodGeliText variant) {
         final String genotype = variant.getBestGenotype().toUpperCase();
-        final String bases = pileup.getBases();
-
         if ( genotype.length() > 2 )
             throw new IllegalArgumentException(String.format("Can only handle diploid genotypes: %s", genotype));
 
-        int on = 0, off = 0;
+        final String bases = pileup.getBases();
+        if ( bases.length() == 0 ) {
+            ratio = 0.0;
+            return new Pair<Integer, Integer>(0, 0);
+        }
 
+        int on = 0, off = 0;
         for ( char base : BaseUtils.BASES ) {
             int count = BasicPileup.countBase(base, bases);
             if ( Utils.countOccurrences(base, genotype) > 0 )