diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantClusteringModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantClusteringModel.java
index 86dd1854f..c5afc5861 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantClusteringModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantClusteringModel.java
@@ -33,5 +33,5 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
 public interface VariantClusteringModel extends VariantOptimizationInterface {
     public void createClusters( final VariantDatum[] data );
-    public double[] applyClusters( final VariantDatum[] data );
+    public void applyClusters( final VariantDatum[] data, final String outputPrefix );
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
index 4673b8b41..76da26164 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
@@ -58,13 +58,20 @@ public class VariantDataManager {
     }
 
     public void normalizeData() {
-        for( int iii = 0; iii < numAnnotations; iii++ ) {
-            final double theMean = mean(data, iii);
-            final double theSTD = standardDeviation(data, theMean, iii);
-            System.out.println( (iii == numAnnotations-1 ? "QUAL" : annotationKeys.get(iii)) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
-            varianceVector[iii] = theSTD * theSTD;
-            for( int jjj=0; jjj<numVariants; jjj++ ) {
-                data[jjj].annotations[iii] = ( data[jjj].annotations[iii] - theMean ) / theSTD;
+        for( int iii = 0; iii < numVariants; iii++ ) {
+            data[iii].originalAnnotations = data[iii].annotations.clone();
+        }
+        for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
+            final double theMean = mean(data, jjj);
+            final double theSTD = standardDeviation(data, theMean, jjj);
+            System.out.println( (jjj == numAnnotations-1 ? "QUAL" : annotationKeys.get(jjj)) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
+            if( theSTD < 1E-8 ) {
+                throw new StingException("Zero variance is a problem: standard deviation = " + theSTD);
+            }
+
+            varianceVector[jjj] = theSTD * theSTD;
+            for( int iii = 0; iii < numVariants; iii++ ) {
+                data[iii].annotations[jjj] = ( data[iii].annotations[jjj] - theMean ) / theSTD;
             }
         }
         isNormalized = true; // Each data point is now [ (x - mean) / standard deviation ]
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
index 01f9bd892..7de62a898 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
@@ -33,6 +33,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
 public class VariantDatum {
     public double[] annotations;
+    public double[] originalAnnotations;
     public boolean isTransition;
     public boolean isKnown;
     public boolean isFiltered;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
index 376b8d7c2..4de6697a9 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+import java.io.PrintStream;
 import java.util.Random;
 
 /*
@@ -33,23 +34,38 @@ import java.util.Random;
  * Date: Feb 26, 2010
  */
 
-public class VariantGaussianMixtureModel extends VariantOptimizationModel implements VariantClusteringModel {
+public final class VariantGaussianMixtureModel extends VariantOptimizationModel implements VariantClusteringModel {
 
-    private final int numGaussians = 128;
+    private final int numGaussians;
+    private final int numIterations;
     private final long RANDOM_SEED = 91801305;
+    private final Random rand = new Random( RANDOM_SEED );
     private final double MIN_PROB = 1E-30;
     private final double MIN_SUM_PROB = 1E-20;
 
-    private final double[][] mu = new double[numGaussians][];
-    private final double[][] sigma = new double[numGaussians][];
-    private final double[] pCluster = new double[numGaussians];
-    final double[] clusterTruePositiveRate = new double[numGaussians];
+    private final double[][] mu;
+    private final double[][] sigma;
+    private final double[] pCluster;
+    private final int[] numMaxClusterKnown;
+    private final int[] numMaxClusterNovel;
+    private final double[] clusterTITV;
+    private final double[] clusterTruePositiveRate;
 
-    public VariantGaussianMixtureModel( VariantDataManager _dataManager, final double _targetTITV ) {
+    public VariantGaussianMixtureModel( VariantDataManager _dataManager, final double _targetTITV, final int _numGaussians, final int _numIterations ) {
        super( _dataManager, _targetTITV );
+        numGaussians = _numGaussians;
+        numIterations = _numIterations;
+
+        mu = new double[numGaussians][];
+        sigma = new double[numGaussians][];
+        pCluster = new double[numGaussians];
+        numMaxClusterKnown = new int[numGaussians];
+        numMaxClusterNovel = new int[numGaussians];
+        clusterTITV = new double[numGaussians];
+        clusterTruePositiveRate = new double[numGaussians];
     }
     
-    public double[] run() {
+    public final void run( final String outputPrefix ) {
 
         // Create the subset of the data to cluster with
         int numSubset = 0;
@@ -58,31 +74,36 @@ public class VariantGaussianMixtureModel extends VariantOptimizationModel implem
                 numSubset++;
             }
         }
-        final VariantDatum[] data = new VariantDatum[numSubset];
+        final VariantDatum[] data = new VariantDatum[numSubset*2];
         int iii = 0;
         for( final VariantDatum datum : dataManager.data ) {
             if( !datum.isKnown ) {
                 data[iii++] = datum;
             }
         }
+        while( iii < numSubset*2 ) { // grab an equal number of known variants at random
+            final VariantDatum datum = dataManager.data[rand.nextInt(dataManager.numVariants)];
+            if( datum.isKnown ) {
+                data[iii++] = datum;
+            }
+        }
 
-        System.out.println("Clustering with " + numSubset + " variants...");
+        System.out.println("Clustering with " + numSubset*2 + " variants...");
         createClusters( data ); // Using a subset of the data
-        System.out.println("Applying clusters to all variants...");
-        return applyClusters( dataManager.data ); // Using all the data
+        System.out.println("Printing out cluster parameters...");
+        printClusters( outputPrefix );
+        System.out.println("Applying clusters to all the variants...");
+        applyClusters( dataManager.data, outputPrefix ); // Using all the data
     }
 
     public final void createClusters( final VariantDatum[] data ) {
 
         final int numVariants = data.length;
         final int numAnnotations = data[0].annotations.length;
-        final int numIterations = 3;
 
         final double[][] pVarInCluster = new double[numGaussians][numVariants];
         final double[] probTi = new double[numGaussians];
         final double[] probTv = new double[numGaussians];
-        final Random rand = new Random( RANDOM_SEED );
-
 
         // loop control variables:
         // iii - loop over data points
@@ -92,7 +113,9 @@ public class VariantGaussianMixtureModel extends VariantOptimizationModel implem
 
         // Set up the initial random Gaussians
         for( int kkk = 0; kkk < numGaussians; kkk++ ) {
-            pCluster[kkk] = 1.0;
+            numMaxClusterKnown[kkk] = 0;
+            numMaxClusterNovel[kkk] = 0;
+            pCluster[kkk] = 1.0 / ((double) numGaussians);
             //final double[] randMu = new double[numAnnotations];
             //for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
             //    randMu[jjj] = data[rand.nextInt(numVariants)].annotations[jjj];
@@ -145,35 +168,116 @@ public class VariantGaussianMixtureModel extends VariantOptimizationModel implem
                     probTv[kkk] += pVarInCluster[kkk][iii];
                 }
             }
+
+            double maxProb = pVarInCluster[0][iii];
+            int maxCluster = 0;
+            for( int kkk = 1; kkk < numGaussians; kkk++ ) {
+                if( pVarInCluster[kkk][iii] > maxProb ) {
+                    maxProb = pVarInCluster[kkk][iii];
+                    maxCluster = kkk;
+                }
+            }
+            if( data[iii].isKnown ) {
+                numMaxClusterKnown[maxCluster]++;
+            } else {
+                numMaxClusterNovel[maxCluster]++;
+            }
         }
         for( int kkk = 0; kkk < numGaussians; kkk++ ) {
-            clusterTruePositiveRate[kkk] = calcTruePositiveRateFromTITV( probTi[kkk] / probTv[kkk] );
+            clusterTITV[kkk] = probTi[kkk] / probTv[kkk];
+            clusterTruePositiveRate[kkk] = calcTruePositiveRateFromTITV( clusterTITV[kkk] );
         }
     }
 
-    public final double[] applyClusters( final VariantDatum[] data ) {
+    private void printClusters( final String outputPrefix ) {
+        try {
+            final PrintStream outputFile = new PrintStream( outputPrefix + ".clusters" );
+            int clusterNumber = 0;
+            final int numAnnotations = mu[0].length;
+            for( int kkk = 0; kkk < numGaussians; kkk++ ) {
+                if( numMaxClusterKnown[kkk] + numMaxClusterNovel[kkk] >= 2000 ) {
+                    outputFile.print(clusterNumber + ",");
+                    outputFile.print(numMaxClusterKnown[kkk] + ",");
+                    outputFile.print(numMaxClusterNovel[kkk] + ",");
+                    outputFile.print(clusterTITV[kkk] + ",");
+                    outputFile.print(clusterTruePositiveRate[kkk] + ",");
+                    for(int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                        outputFile.print(mu[kkk][jjj] + ",");
+                    }
+                    for(int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                        outputFile.print(sigma[kkk][jjj] + ",");
+                    }
+                    outputFile.println(-1);
+                    clusterNumber++;
+                }
+            }
+        } catch (Exception e) {
+            e.printStackTrace();
+            System.exit(-1);
+        }
+    }
+
+    public final void applyClusters( final VariantDatum[] data, final String outputPrefix ) {
 
         final int numVariants = data.length;
+        final int numAnnotations = data[0].annotations.length;
 
         final double[] pTrueVariant = new double[numVariants];
-        final double[][] pVarInCluster = new double[numGaussians][numVariants];
-
-        /////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-        // Expectation Step (calculate the probability that each data point is in each cluster)
-        /////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-        evaluateGaussians( data, pVarInCluster );
+        final double[] pVarInCluster = new double[numGaussians];
+        final int[] clusterAssignment = new int[numVariants];
 
         /////////////////////////////////////////////////////////////////////////////////////////////////////////////////
         // Evaluate each variant using the probability of being in each cluster and that cluster's true positive rate
         /////////////////////////////////////////////////////////////////////////////////////////////////////////////////
         for( int iii = 0; iii < numVariants; iii++ ) {
+            evaluateGaussiansForSingleVariant( data[iii], pVarInCluster );
+
             pTrueVariant[iii] = 0.0;
             for( int kkk = 0; kkk < numGaussians; kkk++ ) {
-                pTrueVariant[iii] += pVarInCluster[kkk][iii] * clusterTruePositiveRate[kkk];
+                pTrueVariant[iii] += pVarInCluster[kkk] * clusterTruePositiveRate[kkk];
             }
+
+            double maxProb = -1.0;//pVarInCluster[0][iii];
+            int maxCluster = -1;
+            for( int kkk = 0; kkk < numGaussians; kkk++ ) {
+                if( numMaxClusterKnown[kkk] + numMaxClusterNovel[kkk] >= 2000 && pVarInCluster[kkk] > maxProb ) {
+                    maxProb = pVarInCluster[kkk];
+                    maxCluster = kkk;
+                }
+            }
+            clusterAssignment[iii] = maxCluster;
         }
 
-        return pTrueVariant;
+        PrintStream outputFile = null;
+        try {
+            outputFile = new PrintStream( outputPrefix + ".data" );
+        } catch (Exception e) {
+            e.printStackTrace();
+            System.exit(-1);
+        }
+        for(int iii = 0; iii < numVariants; iii++) {
+            outputFile.print(pTrueVariant[iii] + ",");
+            outputFile.print(clusterAssignment[iii] + ",");
+            for(int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                outputFile.print(data[iii].originalAnnotations[jjj] + ",");
+            }
+            outputFile.println( (data[iii].isTransition ? 1 : 0)
+                    + "," + (data[iii].isKnown? 1 : 0)
+                    + "," + (data[iii].isFiltered ? 1 : 0));
+        }
+
+        try {
+            outputFile = new PrintStream( outputPrefix + ".optimize" );
+        } catch (Exception e) {
+            e.printStackTrace();
+            System.exit(-1);
+        }
+        for(int iii = 0; iii < numVariants; iii++) {
+            outputFile.print(String.format("%.4f",pTrueVariant[iii]) + ",");
+            outputFile.println( (data[iii].isTransition ? 1 : 0)
+                    + "," + (data[iii].isKnown? 1 : 0)
+                    + "," + (data[iii].isFiltered ? 1 : 0));
+        }
     }
 
 
@@ -207,6 +311,34 @@ public class VariantGaussianMixtureModel extends VariantOptimizationModel implem
     }
 
 
+    private void evaluateGaussiansForSingleVariant( final VariantDatum datum, final double[] pVarInCluster ) {
+
+        final int numAnnotations = datum.annotations.length;
+
+        double sumProb = 0.0;
+        for( int kkk = 0; kkk < numGaussians; kkk++ ) {
+            double sum = 0.0;
+            for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                sum += ( (datum.annotations[jjj] - mu[kkk][jjj]) * (datum.annotations[jjj] - mu[kkk][jjj]) )
+                        / sigma[kkk][jjj];
+            }
+            pVarInCluster[kkk] = pCluster[kkk] * Math.exp( -0.5 * sum );
+
+            if( pVarInCluster[kkk] < MIN_PROB) { // Very small numbers are a very big problem
+                pVarInCluster[kkk] = MIN_PROB;
+            }
+
+            sumProb += pVarInCluster[kkk];
+        }
+
+        if( sumProb > MIN_SUM_PROB ) { // Very small numbers are a very big problem
+            for( int kkk = 0; kkk < numGaussians; kkk++ ) {
+                pVarInCluster[kkk] /= sumProb;
+            }
+        }
+    }
+
+
     private void maximizeGaussians( final VariantDatum[] data, final double[][] pVarInCluster ) {
 
         final int numVariants = data.length;
@@ -253,9 +385,75 @@ public class VariantGaussianMixtureModel extends VariantOptimizationModel implem
                 }
             }
 
-            pCluster[kkk] = sumProb / numVariants; // BUGBUG: Experiment with this, want to keep many clusters alive
-            // Perhaps replace the cluster with a new random draw once pCluster gets too small
-            //  and break up a large cluster with examples drawn from that cluster
+            pCluster[kkk] = sumProb / numVariants;
         }
+
+        // Clean up extra big or extra small clusters
+        for( int kkk = 0; kkk < numGaussians; kkk++ ) {
+            if( pCluster[kkk] > 0.45 ) { // This is a very large cluster compared to all the others
+                System.out.println("Very large cluster!");
+                final int numToReplace = 4;
+                final double[] savedSigma = sigma[kkk];
+                for( int rrr = 0; rrr < numToReplace; rrr++ ) {
+                    // Find an example variant in the large cluster, drawn randomly
+                    int randVarIndex = -1;
+                    boolean foundVar = false;
+                    while( !foundVar ) {
+                        randVarIndex = rand.nextInt( numVariants );
+                        final double probK = pVarInCluster[kkk][randVarIndex];
+                        boolean inClusterK = true;
+                        for( int ccc = 0; ccc < numGaussians; ccc++ ) {
+                            if( pVarInCluster[ccc][randVarIndex] > probK ) {
+                                inClusterK = false;
+                                break;
+                            }
+                        }
+                        if( inClusterK ) { foundVar = true; }
+                    }
+
+                    // Find a place to put the example variant
+                    if( rrr == 0 ) { // Replace the big cluster that kicked this process off
+                        mu[kkk] = data[randVarIndex].annotations;
+                        //sigma[kkk] = savedSigma;
+                        pCluster[kkk] = 1.0 / ((double) numGaussians);
+                    } else { // Replace the cluster with the minimum prob
+                        double minProb = pCluster[0];
+                        int minClusterIndex = 0;
+                        for( int ccc = 1; ccc < numGaussians; ccc++ ) {
+                            if( pCluster[ccc] < minProb ) {
+                                minProb = pCluster[ccc];
+                                minClusterIndex = ccc;
+                            }
+                        }
+                        mu[minClusterIndex] = data[randVarIndex].annotations;
+                        sigma[minClusterIndex] = savedSigma;
+                        for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                            sigma[minClusterIndex][jjj] += -0.02 + 0.04 * rand.nextDouble();
+                        }
+                        pCluster[minClusterIndex] = 1.0 / ((double) numGaussians);
+                    }
+                }
+            }
+        }
+
+        for( int kkk = 0; kkk < numGaussians; kkk++ ) {
+            if( pCluster[kkk] < 0.05 * (1.0 / ((double) numGaussians)) ) { // This is a very small cluster compared to all the others
+                System.out.println("Very small cluster!");
+                pCluster[kkk] = 1.0 / ((double) numGaussians);
+                mu[kkk] = data[rand.nextInt(numVariants)].annotations;
+                final double[] randSigma = new double[numAnnotations];
+                if( dataManager.isNormalized ) {
+                    for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                        randSigma[jjj] = 0.9 + 0.2 * rand.nextDouble();
+                    }
+                } else { // BUGBUG: if not normalized then the varianceVector hasn't been calculated --> null pointer
+                    for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
+                        randSigma[jjj] = dataManager.varianceVector[jjj] + ((1.0 + rand.nextDouble()) * 0.01 * dataManager.varianceVector[jjj]);
+                    }
+                }
+                sigma[kkk] = randSigma;
+            }
+        }
+
     }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java
index 7386f7025..45214b47e 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java
@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+import java.io.PrintStream;
+
 /*
  * Copyright (c) 2010 The Broad Institute
  *
@@ -31,13 +33,13 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
  * Date: Mar 1, 2010
  */
 
-public class VariantNearestNeighborsModel extends VariantOptimizationModel {
+public final class VariantNearestNeighborsModel extends VariantOptimizationModel {
 
     public VariantNearestNeighborsModel( VariantDataManager _dataManager, final double _targetTITV ) {
        super( _dataManager, _targetTITV );
     }
     
-    public double[] run() {
+    public void run( final String outputPrefix ) {
 
         final int numVariants = dataManager.numVariants;
 
@@ -52,6 +54,7 @@ public class VariantNearestNeighborsModel extends VariantOptimizationModel {
             pTrueVariant[iii] = calcTruePositiveRateFromTITV( vTree.calcNeighborhoodTITV( dataManager.data[iii] ) );
         }
 
-        return pTrueVariant;
+        //BUGBUG: need to output pTrueVariant and other metrics in this method
+        //return pTrueVariant;
     }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java
index 33fcb52ca..9724d7907 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java
@@ -32,5 +32,5 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
  */
 
 public interface VariantOptimizationInterface {
-    public double[] run();
+    public void run( String outputPrefix );
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java
index ad904d54d..aee28491e 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java
@@ -40,7 +40,7 @@ public abstract class VariantOptimizationModel implements VariantOptimizationInt
         targetTITV = _targetTITV;
     }
 
-    public double calcTruePositiveRateFromTITV( double titv ) {
+    public final double calcTruePositiveRateFromTITV( double titv ) {
         if( titv > targetTITV ) { titv -= 2.0f*(titv-targetTITV); }
         if( titv < 0.5 ) { titv = 0.5; }
         return ( (titv - 0.5) / (targetTITV - 0.5) );
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java
index 5268059a1..ad8b57093 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java
@@ -9,8 +9,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.ExpandingArrayList;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
-import java.io.PrintStream;
-
 /*
  * Copyright (c) 2010 The Broad Institute
  *
@@ -51,14 +49,21 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Argument(fullName = "target_titv", shortName="titv", doc="The target Ti/Tv ratio towards which to optimize. (~~2.2 for whole genome experiments)", required=true)
+    @Argument(fullName="target_titv", shortName="titv", doc="The target Ti/Tv ratio towards which to optimize. (~~2.2 for whole genome experiments)", required=true)
     private double TARGET_TITV = 2.12;
-    //@Argument(fullName = "filter_output", shortName="filter", doc="If specified the optimizer will not only update the QUAL field of the output VCF file but will also filter the variants", required=false)
+    //@Argument(fullName="filter_output", shortName="filter", doc="If specified the optimizer will not only update the QUAL field of the output VCF file but will also filter the variants", required=false)
     //private boolean FILTER_OUTPUT = false;
-    @Argument(fullName = "ignore_input_filters", shortName="ignoreFilters", doc="If specified the optimizer will use variants even if the FILTER column is marked in the VCF file", required=false)
+    @Argument(fullName="ignore_input_filters", shortName="ignoreFilters", doc="If specified the optimizer will use variants even if the FILTER column is marked in the VCF file", required=false)
     private boolean IGNORE_INPUT_FILTERS = false;
-    @Argument(fullName = "exclude_annotation", shortName = "exclude", doc = "The names of the annotations which should be excluded from the calculations", required = false)
+    @Argument(fullName="exclude_annotation", shortName="exclude", doc="The names of the annotations which should be excluded from the calculations", required=false)
     private String[] EXCLUDED_ANNOTATIONS = null;
+    @Argument(fullName="output", shortName="output", doc="The output file name", required=false)
+    private String OUTPUT_FILE = "optimizer.data";
+    @Argument(fullName="numGaussians", shortName="nG", doc="The number of Gaussians to be used in the Gaussian mixture model", required=false)
+    private int NUM_GAUSSIANS = 32;
+    @Argument(fullName="numIterations", shortName="nI", doc="The number of iterations to be performed in the Gaussian mixture model", required=false)
+    private int NUM_ITERATIONS = 5; //BUGBUG: should automatically decided when to stop by looking at how entropy changes with each iteration
+
 
     /////////////////////////////
     // Private Member Variables
@@ -118,7 +123,6 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
                         value = Double.parseDouble( (String)vc.getAttribute( key, "0.0" ) );
                     } catch( NumberFormatException e ) {
                         // do nothing, default value is 0.0,
-                        // BUGBUG: annotations with zero variance should be ignored
                     }
                     annotationValues[iii++] = value;
                 }
@@ -155,7 +159,7 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
 
     public void onTraversalDone( ExpandingArrayList<VariantDatum> reduceSum ) {
 
-        final VariantDataManager dataManager = new VariantDataManager( reduceSum, annotationKeys );
+        final VariantDataManager dataManager = new VariantDataManager( reduceSum, annotationKeys);
         reduceSum.clear(); // Don't need this ever again, clean up some memory
 
         logger.info( "There are " + dataManager.numVariants + " variants and " + dataManager.numAnnotations + " annotations.");
@@ -163,26 +167,9 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
 
         dataManager.normalizeData(); // Each data point is now [ (x - mean) / standard deviation ]
 
-        final VariantOptimizationModel gmm = new VariantGaussianMixtureModel( dataManager, TARGET_TITV );
-        final double[] p = gmm.run();
-
-        // BUGBUG: Change to call a second ROD walker to output the new VCF file with new qual fields and filters
-        // Intermediate cluster ROD can be analyzed to assess clustering performance
-        try {
-            final PrintStream out = new PrintStream("gmm128clusterNovel.data"); // Parse in Matlab to create performance plots
-            for(int iii = 0; iii < dataManager.numVariants; iii++) {
-                out.print(p[iii] + "\t");
-                out.println( (dataManager.data[iii].isTransition ? 1 : 0)
-                        + "\t" + (dataManager.data[iii].isKnown? 1 : 0)
-                        + "\t" + (dataManager.data[iii].isFiltered ? 1 : 0) );
-            }
-
-
-        } catch (Exception e) {
-            e.printStackTrace();
-            System.exit(-1);
-        }
-
+        // Create either the Gaussian Mixture Model or the Nearest Neighbors model and run it
+        final VariantOptimizationModel gmm = new VariantGaussianMixtureModel( dataManager, TARGET_TITV, NUM_GAUSSIANS, NUM_ITERATIONS  );
+        gmm.run( OUTPUT_FILE );
     }
 
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java
index 02b4c35c3..fa0e19c72 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java
@@ -49,7 +49,7 @@ public class VariantTreeNode {
         cutValue = -1;
     }
 
-    public void cutData( final VariantDatum[] data, final int depth, final int lastCutDepth, final int numAnnotations ) {
+    public final void cutData( final VariantDatum[] data, final int depth, final int lastCutDepth, final int numAnnotations ) {
 
         cutDim = depth % numAnnotations;