diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index c379b34dc..da077ff02 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -451,12 +451,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     public ActivityProfileState isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) {
 
         if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
-            for( final VariantContext vc : tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()) ) {
-                if( !allelesToGenotype.contains(vc) ) {
-                    allelesToGenotype.add(vc); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object
-                }
-            }
-            if( tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ) {
+            final VariantContext vcFromAllelesRod = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, ref.getLocus(), false, logger, UG_engine.getUAC().alleles);
+            if( vcFromAllelesRod != null ) {
+                allelesToGenotype.add(vcFromAllelesRod); // save for later for processing during the ActiveRegion's map call. Should be folded into a RefMetaDataTracker object
                 return new ActivityProfileState(ref.getLocus(), 1.0);
             }
         }