diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
index 52402ad8a..87c614bda 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
@@ -4,6 +4,7 @@ import Jama.Matrix;
 import org.apache.commons.math.special.Gamma;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Arrays;
 import java.util.List;
@@ -88,14 +89,24 @@ public class MultivariateGaussian {
         }
     }
 
+    private void precomputeInverse() {
+        try {
+            cachedSigmaInverse = sigma.inverse();
+        } catch( Exception e ) {
+            throw new UserException("Error during clustering. Most likely there are too few variants used during Gaussian mixture modeling.");
+        }
+    }
+
+
     public void precomputeDenominatorForEvaluation() {
-        cachedSigmaInverse = sigma.inverse();
+        precomputeInverse();
         cachedDenomLog10 = Math.log10(Math.pow(2.0 * Math.PI, -1.0 * ((double) mu.length) / 2.0)) + Math.log10(Math.pow(sigma.det(), -0.5)) ;
     }
 
     public void precomputeDenominatorForVariationalBayes( final double sumHyperParameterLambda ) {
+
         // Variational Bayes calculations from Bishop
-        cachedSigmaInverse = sigma.inverse();
+        precomputeInverse();
         cachedSigmaInverse.timesEquals( hyperParameter_a );
         double sum = 0.0;
         for(int jjj = 1; jjj <= mu.length; jjj++) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 3c4985d92..c523a8337 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -118,13 +118,21 @@ public class VariantDataManager {
             }
         }
         logger.info( "Training with " + trainingData.size() + " variants after standard deviation thresholding." );
+        if( trainingData.size() < )
         return trainingData;
     }
 
-    public ExpandingArrayList<VariantDatum> selectWorstVariants( final double bottomPercentage ) {
+    public ExpandingArrayList<VariantDatum> selectWorstVariants( double bottomPercentage, final int minimumNumber ) {
         Collections.sort( data );
         final ExpandingArrayList<VariantDatum> trainingData = new ExpandingArrayList<VariantDatum>();
-        final int numToAdd = Math.round((float)bottomPercentage * data.size());
+        final int numToAdd = Math.max( minimumNumber, Math.round((float)bottomPercentage * data.size()) );
+        if( numToAdd > data.size() ) {
+            throw new UserException.BadInput("Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadVariants arugment but this is unsafe.");
+        }
+        if( numToAdd == minimumNumber ) {
+            logger.warn("WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.");
+            bottomPercentage = ((float) numToAdd) / ((float) data.size());
+        }
         int index = 0;
         int numAdded = 0;
         while( numAdded < numToAdd ) {
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 fb6da5ed3..85336afa4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -225,7 +225,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         dataManager.normalizeData(); // Each data point is now (x - mean) / standard deviation
         final GaussianMixtureModel goodModel = engine.generateModel( dataManager.getTrainingData() );
         engine.evaluateData( dataManager.getData(), goodModel, false );
-        final GaussianMixtureModel badModel = engine.generateModel( dataManager.selectWorstVariants( VRAC.PERCENT_BAD_VARIANTS ) );
+        final GaussianMixtureModel badModel = engine.generateModel( dataManager.selectWorstVariants( VRAC.PERCENT_BAD_VARIANTS, VRAC.MIN_NUM_BAD_VARIANTS ) );
         engine.evaluateData( dataManager.getData(), badModel, true );
 
         final ExpandingArrayList<VariantDatum> randomData = dataManager.getRandomDataForPlotting( 6000 );
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index 7a524f259..e177cebab 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -36,4 +36,6 @@ public class VariantRecalibratorArgumentCollection {
     public double PRIOR_COUNTS = 20.0;
     @Argument(fullName="percentBadVariants", shortName="percentBad", doc="What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.", required=false)
     public double PERCENT_BAD_VARIANTS = 0.015;
+    @Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary.", required=false)
+    public int MIN_NUM_BAD_VARIANTS = 2000;
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
index 21b7f1bdf..e87048a13 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
@@ -32,9 +32,6 @@ public class VariantRecalibratorEngine {
     }
 
     public GaussianMixtureModel generateModel( final List<VariantDatum> data ) {
-        if( data.size() < 1500 ) {
-            logger.warn("WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.");
-        }
         final GaussianMixtureModel model = new GaussianMixtureModel( VRAC.MAX_GAUSSIANS, data.get(0).annotations.length, VRAC.SHRINKAGE, VRAC.DIRICHLET_PARAMETER, VRAC.PRIOR_COUNTS );
         variationalBayesExpectationMaximization( model, data );
         return model;
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 b44615c6b..9267276fd 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -48,6 +48,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -L 20:1,000,000-40,000,000" +
                         " -an QD -an HaplotypeScore -an HRun" +
                         " -percentBad 0.07" +
+                        " --minNumBadVariants 0" +
                         " --trustAllPolymorphic" + // for speed
                         " -recalFile %s" +
                         " -tranchesFile %s",