diff --git a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
index a89bad2fd..e62a7e512 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
@@ -16,9 +16,6 @@ import java.util.regex.Pattern;
  * Time: 12:38 PM
  */
 public class MendelianViolation {
-
-
-
     String sampleMom;
     String sampleDad;
     String sampleChild;
@@ -31,22 +28,15 @@ public class MendelianViolation {
 
     private static Pattern FAMILY_PATTERN = Pattern.compile("(.*)\\+(.*)=(.*)");
 
-    static final int[] mvOffsets = new int[] { 1,2,5,6,8,11,15,18,20,21,24,25 };
-    static final int[] nonMVOffsets = new int[]{ 0,3,4,7,9,10,12,13,14,16,17,19,22,23,26 };
-
-
     public String getSampleMom() {
         return sampleMom;
     }
-
     public String getSampleDad() {
         return sampleDad;
     }
-
     public String getSampleChild() {
         return sampleChild;
     }
-
     public double getMinGenotypeQuality() {
         return minGenotypeQuality;
     }
@@ -130,7 +120,7 @@ public class MendelianViolation {
      * @return False if we can't determine (lack of information), or it's not a violation. True if it is a violation.
      *
      */
-    public boolean isViolation (VariantContext vc)
+    public boolean isViolation(VariantContext vc)
     {
         return setAlleles(vc) && isViolation();
     }
@@ -144,42 +134,4 @@ public class MendelianViolation {
             return false;
         return true;
     }
-
-    /**
-     * @return the likelihood ratio for a mendelian violation
-     */
-    public double violationLikelihoodRatio(VariantContext vc) {
-        double[] logLikAssignments = new double[27];
-        // the matrix to set up is
-        // MOM   DAD    CHILD
-        //                    |-  AA
-        //   AA     AA    |    AB
-        //                    |-   BB
-        //                    |- AA
-        //  AA     AB     |   AB
-        //                    |- BB
-        // etc. The leaves are counted as 0-11 for MVs and 0-14 for non-MVs
-        double[] momGL = vc.getGenotype(sampleMom).getLikelihoods().getAsVector();
-        double[] dadGL = vc.getGenotype(sampleDad).getLikelihoods().getAsVector();
-        double[] childGL = vc.getGenotype(sampleChild).getLikelihoods().getAsVector();
-        int offset = 0;
-        for ( int oMom = 0; oMom < 3; oMom++ ) {
-            for ( int oDad = 0; oDad < 3; oDad++ ) {
-                for ( int oChild = 0; oChild < 3; oChild ++ ) {
-                    logLikAssignments[offset++] = momGL[oMom] + dadGL[oDad] + childGL[oChild];
-                }
-            }
-        }
-        double[] mvLiks = new double[12];
-        double[] nonMVLiks = new double[15];
-        for ( int i = 0; i < 12; i ++ ) {
-            mvLiks[i] = logLikAssignments[mvOffsets[i]];
-        }
-
-        for ( int i = 0; i < 15; i++) {
-            nonMVLiks[i] = logLikAssignments[nonMVOffsets[i]];
-        }
-
-        return MathUtils.log10sumLog10(mvLiks) - MathUtils.log10sumLog10(nonMVLiks);
-    }
 }