diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 78d7d14f0..ffcaad54c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -231,23 +231,15 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
             //System.out.println(new String(ref.getBases()));
             byte[] refBases = Arrays.copyOfRange(ref.getBases(),startIdxInReference,startIdxInReference+dLen);
-            boolean ok = true;
-            for (int i=0; i < refBases.length; i++)
-                if (!BaseUtils.isRegularBase(refBases[i]))
-                    ok = false;
 
-            if (ok) {
+            if (Allele.acceptableAlleleBases(refBases)) {
                 refAllele = Allele.create(refBases,true);
                 altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
             }
         }
         else {
             // insertion case
-            boolean ok = true;
-            for (int i=0; i < bestAltAllele.length(); i++)
-                if (!BaseUtils.isRegularBase(bestAltAllele.getBytes()[i]))
-                    ok = false;
-            if (ok)  {
+            if (Allele.acceptableAlleleBases(bestAltAllele))  {
                 refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
                 altAllele = Allele.create(bestAltAllele, false);
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 0cb942ab3..2f4ae3e2c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -203,6 +203,10 @@ public class UnifiedGenotyperEngine {
                 return null;
             vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
         } else {
+            // deal with bad/non-standard reference bases
+            if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )
+                return null;
+
             Set<Allele> alleles = new HashSet<Allele>();
             alleles.add(Allele.create(ref.getBase(), true));
             vc = new VariantContext("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), alleles);