diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
index 5eeadddae..f6559f666 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
@@ -94,6 +94,10 @@ public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends Gener
             haplotypeMap.clear();
         }
         IndelGenotypeLikelihoodsCalculationModel.getHaplotypeMapFromAlleles(alleles, ref, ref.getLocus(), haplotypeMap);
+
+        // sanity check: if haplotype map couldn't be created, clear allele list
+        if (haplotypeMap.isEmpty())
+            alleles.clear();
         return alleles;
 
     }