diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 2b84e02a6..730b9de93 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -63,10 +63,13 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
     protected Logger logger;
     protected PrintStream verboseWriter;
 
-    protected AlleleFrequencyCalculationModel(int N, Logger logger, PrintStream verboseWriter) {
+    protected boolean useReferenceSampleOptimization;
+
+    protected AlleleFrequencyCalculationModel(int N, Logger logger, PrintStream verboseWriter, boolean useReferenceSampleOptimization) {
         this.N = N;
         this.logger = logger;
         this.verboseWriter = verboseWriter;
+        this.useReferenceSampleOptimization = useReferenceSampleOptimization;
         AFMatrix = new AlleleFrequencyMatrix(N);
         refCalls = new HashSet<BiallelicGenotypeLikelihoods>();
     }
@@ -171,7 +174,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
         AFMatrix.clear();
 
         for ( BiallelicGenotypeLikelihoods GL : GLs.values() ) {
-            if ( isClearRefCall(GL) ) {
+            if ( useReferenceSampleOptimization && isClearRefCall(GL) ) {
                 refCalls.add(GL);
             } else {
                 AFMatrix.setLikelihoods(GL.getPosteriors(), GL.getSample());
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 20b53c185..dfa455a69 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -47,7 +47,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
     private static final double LOGEPS = -300;
 
     protected ExactAFCalculationModel(int N, Logger logger, PrintStream verboseWriter) {
-        super(N, logger, verboseWriter);
+        super(N, logger, verboseWriter, true);
     }
 
     public void getLog10PNonRef(RefMetaDataTracker tracker,
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
index 6977fb0d8..edef58d13 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -41,7 +41,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
     protected static final double LOG10_OPTIMIZATION_EPSILON = 8.0;
 
     protected GridSearchAFEstimation(int N, Logger logger, PrintStream verboseWriter) {
-        super(N, logger, verboseWriter);
+        super(N, logger, verboseWriter, false);
     }
 
     public void getLog10PNonRef(RefMetaDataTracker tracker,