diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
index cc7bcc5e1..3378027ef 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
@@ -49,7 +49,12 @@ import java.util.regex.Pattern;
 public final class VariantGaussianMixtureModel extends VariantOptimizationModel {
 
     protected final static Logger logger = Logger.getLogger(VariantGaussianMixtureModel.class);
-    
+
+    /**
+     * Est. FP rate for singleton calls.  Used to estimate FP rate as a function of AC
+     */
+    private double singletonFPRate = -1;
+
     public final VariantDataManager dataManager;
     private final int maxGaussians;
     private final int maxIterations;
@@ -152,7 +157,9 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         alleleCountFactorArray = new double[alleleCountLines.size() + 1];
         for( final String line : alleleCountLines ) {
             final String[] vals = line.split(",");
-            alleleCountFactorArray[Integer.parseInt(vals[1])] = Double.parseDouble(vals[2]);
+            int i = Integer.parseInt(vals[1]);
+            alleleCountFactorArray[i] = Double.parseDouble(vals[2]);
+            double oldACPrior = alleleCountFactorArray[i];
         }
 
         int kkk = 0;
@@ -315,8 +322,16 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         }
     }
 
+    public void setSingletonFPRate(double rate) {
+        this.singletonFPRate = rate;
+    }
+
     public final double getAlleleCountPrior( final int alleleCount ) {
-        return alleleCountFactorArray[alleleCount];
+        if ( this.singletonFPRate == -1 )
+            return alleleCountFactorArray[alleleCount];
+        else {
+            return 1 - Math.pow(singletonFPRate, alleleCount);
+        }
     }
 
     private void initializeUsingKMeans( final VariantDatum[] data ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index eb72f6db7..cf8460111 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -89,6 +89,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     private String PATH_TO_RESOURCES = "R/";
     @Argument(fullName="quality_step", shortName="qStep", doc="Resolution in QUAL units for optimization and tranche calculations", required=false)
     private double QUAL_STEP = 0.1;
+    @Argument(fullName="singleton_fp_rate", shortName="fp_rate", doc="Prior expectation that a singleton call would be a FP", required=false)
+    private double SINGLETON_FP_RATE = -1;
 
     /////////////////////////////
     // Private Member Variables
@@ -113,6 +115,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         switch (OPTIMIZATION_MODEL) {
             case GAUSSIAN_MIXTURE_MODEL:
                 theModel = new VariantGaussianMixtureModel( TARGET_TITV, CLUSTER_FILENAME, BACKOFF_FACTOR );
+                if ( SINGLETON_FP_RATE != -1 )
+                    theModel.setSingletonFPRate(SINGLETON_FP_RATE);
                 break;
             //case K_NEAREST_NEIGHBORS:
             //    theModel = new VariantNearestNeighborsModel( dataManager, TARGET_TITV, NUM_KNN );