diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 59f241cdb..e1a1ed6d2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -120,6 +120,11 @@ public class LikelihoodCalculationEngine {
 
             for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
                 final Haplotype haplotype = haplotypes.get(jjj);
+
+                // TODO -- need to test against a reference/position with non-standard bases
+                if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) )
+                    continue;
+
                 final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) );
                 previousHaplotypeSeen = haplotype;