diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index 16420b6fd..bb0b3bed9 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -112,7 +112,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
     private ExpandingArrayList<String> annotationKeys;
     private Set<String> ignoreInputFilterSet = null;
     private Set<String> inputNames = new HashSet<String>();
-
+    VariantGaussianMixtureModel theModel = new VariantGaussianMixtureModel();
 
     //---------------------------------------------------------------------------------------------------------------
     //
@@ -174,7 +174,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
                 if( !vc.isFiltered() || IGNORE_ALL_INPUT_FILTERS || (ignoreInputFilterSet != null && ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
                     int iii = 0;
                     for( final String key : annotationKeys ) {
-                        annotationValues[iii++] = VariantGaussianMixtureModel.decodeAnnotation( key, vc, true );
+                        annotationValues[iii++] = theModel.decodeAnnotation( key, vc, true );
                     }
 
                     final VariantDatum variantDatum = new VariantDatum();
@@ -234,7 +234,6 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
         dataManager.normalizeData(); // Each data point is now [ (x - mean) / standard deviation ]
 
         // Create either the Gaussian Mixture Model or the Nearest Neighbors model and run it
-        VariantGaussianMixtureModel theModel;
         switch (OPTIMIZATION_MODEL) {
             case GAUSSIAN_MIXTURE_MODEL:
                 theModel = new VariantGaussianMixtureModel( dataManager, MAX_GAUSSIANS, MAX_ITERATIONS, FORCE_INDEPENDENT,
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 7558b35db..b451e4edc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
@@ -60,7 +60,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
     private final int maxGaussians;
     private final int maxIterations;
     private final static long RANDOM_SEED = 91801305;
-    private final static Random rand = new Random( RANDOM_SEED );
+    private final Random rand = new Random( RANDOM_SEED );
     private final double MIN_PROB_CONVERGENCE = 1E-5;
 
     private final double SHRINKAGE;
@@ -85,6 +85,23 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
     private static final Pattern ANNOTATION_PATTERN = Pattern.compile("^@!ANNOTATION.*");
     private static final Pattern CLUSTER_PATTERN = Pattern.compile("^@!CLUSTER.*");
 
+    public VariantGaussianMixtureModel() {
+        dataManager = null;
+        maxGaussians = 0;
+        maxIterations = 0;
+        SHRINKAGE = 0;
+        DIRICHLET_PARAMETER = 0;
+        FORCE_INDEPENDENT_ANNOTATIONS = false;
+        mu = null;
+        sigma = null;
+        sigmaInverse = null;
+        determinant = null;
+        stdThreshold = 0;
+        hyperParameter_a = null;
+        hyperParameter_b = null;
+        hyperParameter_lambda = null;
+    }
+
     public VariantGaussianMixtureModel( final VariantDataManager _dataManager, final int _maxGaussians, final int _maxIterations,
                                         final boolean _forceIndependent, final double _stdThreshold, final double _shrinkage, final double _dirichlet) {
         dataManager = _dataManager;
@@ -398,7 +415,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         }
     }
 
-    public static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter ) {
+    public double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter ) {
         double value;
         //if( annotationKey.equals("AB") && !vc.getAttributes().containsKey(annotationKey) ) {
         //    value = (0.5 - 0.005) + (0.01 * rand.nextDouble()); // HomVar calls don't have an allele balance
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 ab34c20ef..426343551 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -14,7 +14,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testGenerateVariantClusters() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "79727fb46bb60be30eae2666e4f792b6" );
+        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "cb3e8d9072d478243c3f9d0ee09fef3b" );
+        e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf", "0d4fee916a886ca98c286d3b7fed0ff6" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String vcf = entry.getKey();
@@ -23,12 +24,13 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
                             " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
+                            " -B:hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
+                            " -weightDBSNP 1.0 -weightHapMap 1.0" +
                             " -T GenerateVariantClusters" +
                             " -B:input,VCF " + vcf +
                             " -L 1:1-100,000,000" +
                             " --ignore_filter GATK_STANDARD" +
                             " -an QD -an HRun -an SB" +
-                            " -weightDBSNP 1.0" +
                             " -clusterFile %s",
                     1, // just one output file
                     Arrays.asList(md5));
@@ -39,18 +41,22 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     @Test
     public void testVariantRecalibrator() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "f2790e2f4f3c23df800c18aaa39b3fde" );
-        
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
+        HashMap<String, List<String>> e = new HashMap<String, List<String>>();
+        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
+                Arrays.asList("ad0868adddb2e837b4fc08f140e4d9c3", "937080353c7e03e11f8a70fc0004bf76","5b89fa5a4edf0080d64230d4103d2b8d")); // Each test checks the md5 of three output files
+        e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf",
+                Arrays.asList("054d3228acfd6b02d24bfcf2fbd280a0", "f7c5c6cff9dd5280b25e24e0591e4cb0","1de1473db5720b882edf1381fa3dd039")); // Each test checks the md5 of three output files
+
+        for ( Map.Entry<String, List<String>> entry : e.entrySet() ) {
             String vcf = entry.getKey();
-            String md5 = entry.getValue();
+            List<String> md5s = entry.getValue();
             String clusterFile = clusterFiles.get(vcf);
             System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
             if ( clusterFile != null ) {
                 WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                         "-R " + b36KGReference +
                                 " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
+                                " -B:hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
                                 " -T VariantRecalibrator" +
                                 " -B:input,VCF " + vcf +
                                 " -L 1:40,000,000-100,000,000" +
@@ -62,7 +68,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " -tranchesFile %s" +
                                 " -reportDatFile %s",                                
                         3, // two output file
-                        Arrays.asList(md5, "d979864c46ae237f52f1002f0ec19b16","ab438d03e276a053d7534056f62c83f3"));
+                        md5s);
                 List<File> result = executeTest("testVariantRecalibrator", spec).getFirst();
                 inputVCFFiles.put(vcf, result.get(0).getAbsolutePath());
                 tranchesFiles.put(vcf, result.get(1).getAbsolutePath());
@@ -75,7 +81,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testApplyVariantCuts() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "d30eafb642a80a00bd82fb4140b5277e" );
+        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "841deca1cb30a5a081cfbaa6f663e22a" );
+        e.put( validationDataLocation + "lowpass.N3.chr1.raw.0.vcf", "6234259e75fd7c1db31566dde1c55a82" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String vcf = entry.getKey();
@@ -95,7 +102,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " -tranchesFile " + tranchesFile,
                         1, // just one output file
                         Arrays.asList(md5));
-                List<File> result = executeTest("testApplyVariantCuts", spec).getFirst();
+                executeTest("testApplyVariantCuts", spec);
             }
         }
     }