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 7e9574a4f..9ea341d92 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -378,8 +378,14 @@ public class UnifiedGenotyperEngine {
 
         int endLoc = calculateEndPos(vc.getAlleles(), vc.getReference(), loc);
 
+        Set<Allele> myAlleles = vc.getAlleles();
+        // strip out the alternate allele if it's a ref call
+        if ( bestAFguess == 0 ) {
+            myAlleles = new HashSet<Allele>(1);
+            myAlleles.add(vc.getReference());
+        }
         VariantContext vcCall = new VariantContext("UG_call", loc.getContig(), loc.getStart(), endLoc,
-                vc.getAlleles(), genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
+                myAlleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
 
         if ( annotationEngine != null ) {
             // first off, we want to use the *unfiltered* context for the annotations
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 3fe089ee5..3aeaf41c8 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -105,8 +105,8 @@ public class
     @Test
     public void testParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-genotype", "683ce57f2fd3acd5f6fe7599c1ace169" );
-        e.put( "-all_bases", "2ddf763c208602693cad942c9ccb804c" );
+        e.put( "-genotype", "4ffcb1e1f20ce175783c32c30deef8db" );
+        e.put( "-all_bases", "3d98205a31a133c11e518e095dc7ab65" );
         e.put( "--min_base_quality_score 26", "5f1cfb9c7f82e6414d5db7aa344813ac" );
         e.put( "--min_mapping_quality_score 26", "6c3ad441f3a23ade292549b1dea80932" );
         e.put( "--max_mismatches_in_40bp_window 5", "5ecaf4281410b67e8e2e164f2ea0d58a" );