diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index e2caf87c8..096aa3af1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -202,14 +202,14 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         // the base was confidently callable
         sum.nBasesCalledConfidently += value.confidentlyCalled ? 1 : 0;
 
-        // can't make a confident variant call here
-        if ( value.vc == null )
+        // can't make a call here
+        if ( !value.shouldEmit )
             return sum;
 
         try {
             // we are actually making a call
             sum.nCallsMade++;
-            writer.add(value.vc, value.refBase);
+            writer.add(value, value.refBase);
         } catch (IllegalArgumentException e) {
             throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
         }
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 f54509c4a..5f9974123 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -297,7 +297,7 @@ public class UnifiedGenotyperEngine {
         // estimate our confidence in a reference call and return
         if ( vc.getNSamples() == 0 )
             return (UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES ?
-                    estimateReferenceConfidence(stratifiedContexts, genotypePriors.getHeterozygosity(), false, 1.0) :
+                    estimateReferenceConfidence(vc, stratifiedContexts, genotypePriors.getHeterozygosity(), false, 1.0) :
                     new VariantCallContext(generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext), refContext.getBase(), false));
 
         // 'zero' out the AFs (so that we don't have to worry if not all samples have reads at this position)
@@ -336,7 +336,7 @@ public class UnifiedGenotyperEngine {
         if ( UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES && !passesEmitThreshold(phredScaledConfidence, bestAFguess) ) {
             // technically, at this point our confidence in a reference call isn't accurately estimated
             //  because it didn't take into account samples with no data, so let's get a better estimate
-            return estimateReferenceConfidence(stratifiedContexts, genotypePriors.getHeterozygosity(), true, 1.0 - PofF);
+            return estimateReferenceConfidence(vc, stratifiedContexts, genotypePriors.getHeterozygosity(), true, 1.0 - PofF);
         }
 
         // create the genotypes
@@ -423,7 +423,7 @@ public class UnifiedGenotyperEngine {
             vcCall = variantContexts.iterator().next(); // we know the collection will always have exactly 1 element.
         }
 
-        VariantCallContext call = new VariantCallContext(vcCall, passesCallThreshold(phredScaledConfidence));
+        VariantCallContext call = new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF));
         call.setRefBase(refContext.getBase());
         return call;
     }
@@ -491,7 +491,7 @@ public class UnifiedGenotyperEngine {
             AFs[i] = AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED;
     }
 
-    private VariantCallContext estimateReferenceConfidence(Map<String, StratifiedAlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) {
+    private VariantCallContext estimateReferenceConfidence(VariantContext vc, Map<String, StratifiedAlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) {
         if ( contexts == null )
             return null;
 
@@ -518,7 +518,7 @@ public class UnifiedGenotyperEngine {
             P_of_ref *= 1.0 - (theta / 2.0) * MathUtils.binomialProbability(0, depth, 0.5);
         }
 
-        return new VariantCallContext(QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING);
+        return new VariantCallContext(vc, QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING, false);
     }
 
     protected void printVerboseData(String pos, VariantContext vc, double PofF, double phredScaledConfidence, double[] normalizedPosteriors) {
@@ -651,6 +651,11 @@ public class UnifiedGenotyperEngine {
         return conf >= UAC.STANDARD_CONFIDENCE_FOR_CALLING;
     }
 
+    protected boolean confidentlyCalled(double conf, double PofF) {
+        return conf >= UAC.STANDARD_CONFIDENCE_FOR_CALLING ||
+                (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES && QualityUtils.phredScaleErrorRate(PofF) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING);
+    }
+
     protected void computeAlleleFrequencyPriors(int N) {
         // calculate the allele frequency priors for 1-N
         double sum = 0.0;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
index f280b75b7..16dac6fbe 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
@@ -35,29 +35,32 @@ import org.broad.tribble.util.variantcontext.VariantContext;
  *
  * Useful helper class to communicate the results of calculateGenotype to framework
  */
-public class VariantCallContext {
-    public VariantContext vc = null;
+public class VariantCallContext extends VariantContext {
     public byte refBase;
 
     // Was the site called confidently, either reference or variant?
     public boolean confidentlyCalled = false;
 
+    // Should this site be emitted?
+    public boolean shouldEmit = true;
+
     VariantCallContext(VariantContext vc, boolean confidentlyCalledP) {
-        this.vc = vc;
+        super(vc);
         this.confidentlyCalled = confidentlyCalledP;
     }
 
+    VariantCallContext(VariantContext vc, boolean confidentlyCalledP, boolean shouldEmit) {
+        super(vc);
+        this.confidentlyCalled = confidentlyCalledP;
+        this.shouldEmit = shouldEmit;
+    }
+
     VariantCallContext(VariantContext vc, byte ref, boolean confidentlyCalledP) {
-        this.vc = vc;
+        super(vc);
         this.refBase = ref;
         this.confidentlyCalled = confidentlyCalledP;
     }
 
-    // blank variant context => we're a ref site
-    VariantCallContext(boolean confidentlyCalledP) {
-        this.confidentlyCalled = confidentlyCalledP;
-    }
-
     public void setRefBase(byte ref) {
         this.refBase = ref;
     }