diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
index 43d5f0b28..34f4bd607 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@@ -17,16 +18,13 @@ import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
- * User: rpoplin, lfran
+ * User: rpoplin, lfran, ebanks
  * Date: 11/14/11
  */
 
-public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implements ExperimentalAnnotation {
+public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implements ExperimentalAnnotation, RodRequiringAnnotation {
 
     private Set<Sample> trios = null;
-    private final static int REF = 0;
-    private final static int HET = 1;
-    private final static int HOM = 2;
     private final static int MIN_NUM_VALID_TRIOS = 5; // don't calculate this population-level statistic if there are less than X trios with full genotype likelihood information
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
@@ -38,10 +36,10 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
             }
         }
 
-        final Map<String,Object> toRet = new HashMap<String,Object>(1);
+        final Map<String, Object> toRet = new HashMap<String, Object>(1);
         final HashSet<Sample> triosToTest = new HashSet<Sample>();
 
-        for( final Sample child : trios) {
+        for( final Sample child : trios ) {
             final boolean hasAppropriateGenotypes = vc.hasGenotype(child.getID()) && vc.getGenotype(child.getID()).hasLikelihoods() &&
                     vc.hasGenotype(child.getPaternalID()) && vc.getGenotype(child.getPaternalID()).hasLikelihoods() &&
                     vc.hasGenotype(child.getMaternalID()) && vc.getGenotype(child.getMaternalID()).hasLikelihoods();
@@ -65,28 +63,54 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
     // Following derivation in http://en.wikipedia.org/wiki/Transmission_disequilibrium_test#A_modified_version_of_the_TDT
     private double calculateTDT( final VariantContext vc, final Set<Sample> triosToTest ) {
 
-        final double nABGivenABandBB = calculateNChildren(vc, triosToTest, HET, HET, HOM) + calculateNChildren(vc, triosToTest, HET, HOM, HET);
-        final double nBBGivenABandBB = calculateNChildren(vc, triosToTest, HOM, HET, HOM) + calculateNChildren(vc, triosToTest, HOM, HOM, HET);
-        final double nAAGivenABandAB = calculateNChildren(vc, triosToTest, REF, HET, HET);
-        final double nBBGivenABandAB = calculateNChildren(vc, triosToTest, HOM, HET, HET);
-        final double nAAGivenAAandAB = calculateNChildren(vc, triosToTest, REF, REF, HET) + calculateNChildren(vc, triosToTest, REF, HET, REF);
-        final double nABGivenAAandAB = calculateNChildren(vc, triosToTest, HET, REF, HET) + calculateNChildren(vc, triosToTest, HET, HET, REF);
+        double nABGivenABandBB = 0.0;
+        double nBBGivenABandBB = 0.0;
+        double nAAGivenABandAB = 0.0;
+        double nBBGivenABandAB = 0.0;
+        double nAAGivenAAandAB = 0.0;
+        double nABGivenAAandAB = 0.0;
+
+        // for each pair of alleles, add the likelihoods
+        int numAlleles = vc.getNAlleles();
+        for ( int allele1 = 0; allele1 < numAlleles; allele1++ ) {
+            for ( int allele2 = allele1 + 1; allele2 < numAlleles; allele2++ ) {
+
+                // TODO -- cache these for better performance
+                final int HOM1index = determineHomIndex(allele1, numAlleles);
+                final int HETindex = HOM1index + (allele2 - allele1);
+                final int HOM2index = determineHomIndex(allele2, numAlleles);
+
+                nABGivenABandBB += calculateNChildren(vc, triosToTest, HETindex, HETindex, HOM2index) + calculateNChildren(vc, triosToTest, HETindex, HOM2index, HETindex);
+                nBBGivenABandBB += calculateNChildren(vc, triosToTest, HOM2index, HETindex, HOM2index) + calculateNChildren(vc, triosToTest, HOM2index, HOM2index, HETindex);
+                nAAGivenABandAB += calculateNChildren(vc, triosToTest, HOM1index, HETindex, HETindex);
+                nBBGivenABandAB += calculateNChildren(vc, triosToTest, HOM2index, HETindex, HETindex);
+                nAAGivenAAandAB += calculateNChildren(vc, triosToTest, HOM1index, HOM1index, HETindex) + calculateNChildren(vc, triosToTest, HOM1index, HETindex, HOM1index);
+                nABGivenAAandAB += calculateNChildren(vc, triosToTest, HETindex, HOM1index, HETindex) + calculateNChildren(vc, triosToTest, HETindex, HETindex, HOM1index);
+            }
+        }
 
         final double numer = (nABGivenABandBB - nBBGivenABandBB) + 2.0 * (nAAGivenABandAB - nBBGivenABandAB) + (nAAGivenAAandAB - nABGivenAAandAB);
         final double denom = (nABGivenABandBB + nBBGivenABandBB) + 4.0 * (nAAGivenABandAB + nBBGivenABandAB) + (nAAGivenAAandAB + nABGivenAAandAB);
         return (numer * numer) / denom;
     }
 
-    private double calculateNChildren( final VariantContext vc, final Set<Sample> triosToTest, final int childIdx, final int parent1Idx, final int parent2Idx ) {
+    private double calculateNChildren( final VariantContext vc, final Set<Sample> triosToTest, final int childIdx, final int momIdx, final int dadIdx ) {
         final double likelihoodVector[] = new double[triosToTest.size()];
         int iii = 0;
         for( final Sample child : triosToTest ) {
             final double[] momGL = vc.getGenotype(child.getMaternalID()).getLikelihoods().getAsVector();
             final double[] dadGL = vc.getGenotype(child.getPaternalID()).getLikelihoods().getAsVector();
             final double[] childGL = vc.getGenotype(child.getID()).getLikelihoods().getAsVector();
-            likelihoodVector[iii++] = momGL[parent1Idx] + dadGL[parent2Idx] + childGL[childIdx];
+            likelihoodVector[iii++] = momGL[momIdx] + dadGL[dadIdx] + childGL[childIdx];
         }
 
         return MathUtils.sumLog10(likelihoodVector);
     }
+    
+    private static int determineHomIndex(final int alleleIndex, int numAlleles) {
+        int result = 0;
+        for ( int i = 0; i < alleleIndex; i++ )
+            result += numAlleles--;
+        return result;
+    }
 }