diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 149fa6e8c..80c85b826 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -155,9 +155,9 @@ public class RecalDataManager {
     }
 
     /**
-     * Loop over all the collapsed tables and turn the recalDatums found there into an empricial quality score
+     * Loop over all the collapsed tables and turn the recalDatums found there into an empirical quality score
      *   that will be used in the sequential calculation in TableRecalibrationWalker
-     * @param smoothing The smoothing paramter that goes into empirical quality score calculation
+     * @param smoothing The smoothing parameter that goes into empirical quality score calculation
      * @param maxQual At which value to cap the quality scores
      */
     public final void generateEmpiricalQualities( final int smoothing, final int maxQual ) {
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 a0efb917f..60b196842 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
@@ -231,16 +231,21 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
             }
         }
 
+        double sumWeight = 0.0;
         for(int iii = 0; iii < numVariants; iii++) {
+            sumWeight += data[iii].weight;           
             for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
-                empiricalMu[jjj] += data[iii].annotations[jjj] / ((double) numVariants);
+                empiricalMu[jjj] += data[iii].annotations[jjj] * data[iii].weight;
             }
         }
+        for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
+            empiricalMu[jjj] /= sumWeight;
+        }
 
         for(int iii = 0; iii < numVariants; iii++) {
             for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
                 for( int ppp = 0; ppp < numAnnotations; ppp++ ) {
-                    if( jjj == ppp ) {
+                    if( jjj == ppp ) {                        
                         sigmaVals[jjj][ppp] = 1.0; //0.01 * numAnnotations;
                     } else {
                         sigmaVals[jjj][ppp] = 0.0;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 3764859cc..60c891f5e 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -29,13 +29,13 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
-            "e14079c3a02c112665a6c194fd4f5d5c",  // cluster file
+            "f65c27ee40053adc72dd0bfbb628e4d7",  // cluster file
             "dce581b880ffb6ea39cbada1ecc95915",  // tranches
             "c3e8a2f43656eab7d847dbf850f844a6",  // recalVCF
             "50f752a72643db9ad0aa94b3fc4e23d6"); // cut VCF
 
     VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf",
-            "b0c0f8c8d9fe3d1ed2bde0b1eb82a22d",  // cluster file
+            "bda8f17cfc19d23e7e51f99e547f4b3d",  // cluster file
             "66edae83c50f4e8601fef7fafba774af",  // tranches
             "0123537e373657386068a534c0f5c91b",  // recalVCF
             "2172368e8585841e5ad96c95d0827c4b"); // cut VCF