diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index ac7c370bf..c767cf783 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -35,7 +35,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -43,7 +42,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -68,9 +66,11 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
 
         final byte refBase = ref.getBase();
         final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase);
+        // handle non-standard reference bases
+        if ( indexOfRefBase == -1 )
+            return null;
         final Allele refAllele = Allele.create(refBase, true);
 
-
         // calculate the GLs
         ArrayList<SampleGenotypeData> GLs = new ArrayList<SampleGenotypeData>(contexts.size());
         for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {