diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index 12b541526..52629277f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -266,6 +266,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
        Map<String, Object> genotypeAttributes = new HashMap<String, Object>();
        genotypeAttributes.putAll(genotype.getAttributes());
        genotypeAttributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, transmissionProb);
+       genotype = Genotype.modifyAttributes(genotype, genotypeAttributes);
 
        boolean isPhased = true;
 
@@ -274,7 +275,6 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
         //If unphased, return original genotype
         for(AlleleType allele : phasedAlleles){
             if(allele == AlleleType.NO_CALL){
-                 genotype = Genotype.modifyAttributes(genotype, genotypeAttributes);
                 return genotype;
             }
             //Otherwise add the appropriate allele
@@ -293,13 +293,8 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
                 alleles.add(altAllele);
             }
         }
-       //TODO: Recalculate GQ field for the new genotype
-       //Remove the GQ attribute as it needs to be recalculated for the new genotype assignment
-       //double[] likelihoods = genotype.getLikelihoods().getAsVector();
 
-       //genotypeAttributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,likelihoods[1]);
-       genotype = Genotype.modifyAttributes(genotype, genotypeAttributes);
-       return new Genotype(genotype.getSampleName(), alleles, genotype.getNegLog10PError(), null, genotype.getAttributes(), isPhased);
+       return new Genotype(genotype.getSampleName(), alleles, genotype.getLikelihoods().getLog10GQ(genotype.getType()), null, genotype.getAttributes(), isPhased);
    }
 
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index 292bc17cd..9ed9b41cc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -25,8 +25,10 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
 import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.jgrapht.util.MathUtil;
 
 import java.util.EnumMap;
 import java.util.Map;
@@ -98,6 +100,7 @@ public class GenotypeLikelihoods {
         return likelihoodsAsString_PLs;
     }
 
+    //Return genotype likelihoods as an EnumMap with Genotypes as keys and likelihoods as values
     public EnumMap<Genotype.Type,Double> getAsMap(boolean normalizeFromLog10){
         //Make sure that the log10likelihoods are set
         double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector();
@@ -108,6 +111,32 @@ public class GenotypeLikelihoods {
         return likelihoodsMap;
     }
 
+    //Return the log10 Genotype Quality (GQ) for the given genotype
+    public double getLog10GQ(Genotype.Type genotype){
+
+        double qual = Double.NEGATIVE_INFINITY;
+        EnumMap<Genotype.Type,Double> likelihoods = getAsMap(false);
+        for(Map.Entry<Genotype.Type,Double> likelihood : likelihoods.entrySet()){
+            if(likelihood.getKey() == genotype)
+                continue;
+            if(likelihood.getValue() > qual)
+                qual = likelihood.getValue();
+
+        }
+
+        qual = likelihoods.get(genotype) - qual;
+
+        if (qual < 0) {
+                // QUAL can be negative if the chosen genotype is not the most likely one individually.
+                // In this case, we compute the actual genotype probability and QUAL is the likelihood of it not being the chosen one
+                double[] normalized = MathUtils.normalizeFromLog10(getAsVector());
+                double chosenGenotype = normalized[genotype.ordinal()-1];
+                qual = -1.0 * Math.log10(1.0 - chosenGenotype);
+        }
+
+        return qual;
+    }
+
     private final static double[] parsePLsIntoLikelihoods(String likelihoodsAsString_PLs) {
         if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
             String[] strings = likelihoodsAsString_PLs.split(",");