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 d3ed46ce8..cf4afbb6d 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
@@ -234,7 +234,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
         finalGenotypes.add(father);
         finalGenotypes.add(child);
 
-        if (mother.isCalled() && father.isCalled() && child.isCalled() && !(mother.isHet() && father.isHet() && child.isHet())) {
+        if (mother.isCalled() && father.isCalled() && child.isCalled()) {
             ArrayList<Genotype> possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother);
             ArrayList<Genotype> possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father);
             ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child);
@@ -265,12 +265,14 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
                 }
             }
 
-            Map<String, Object> attributes = new HashMap<String, Object>();
-            attributes.putAll(bestChildGenotype.getAttributes());
-            attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
-            bestChildGenotype = Genotype.modifyAttributes(bestChildGenotype, attributes);
+            if (!(bestMotherGenotype.isHet() && bestFatherGenotype.isHet() && bestChildGenotype.isHet())) {
+                Map<String, Object> attributes = new HashMap<String, Object>();
+                attributes.putAll(bestChildGenotype.getAttributes());
+                attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
+                bestChildGenotype = Genotype.modifyAttributes(bestChildGenotype, attributes);
 
-            finalGenotypes = getPhasedGenotypes(bestMotherGenotype, bestFatherGenotype, bestChildGenotype);
+                finalGenotypes = getPhasedGenotypes(bestMotherGenotype, bestFatherGenotype, bestChildGenotype);
+            }
         }
 
         return finalGenotypes;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index fe3173506..3867aa958 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -67,7 +67,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     @Argument(fullName="stratificationModule", shortName="ST", doc="One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)", required=false)
     protected String[] STRATIFICATIONS_TO_USE = {};
 
-    @Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)")
+    @Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)", required=false)
     protected Boolean NO_STANDARD_STRATIFICATIONS = false;
 
     @Argument(fullName="onlyVariantsOfType", shortName="VT", doc="If provided, only variants of these types will be considered during the evaluation, in ", required=false)
@@ -77,7 +77,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
     @Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)", required=false)
     protected String[] MODULES_TO_USE = {};
 
-    @Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)")
+    @Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)", required=false)
     protected Boolean NO_STANDARD_MODULES = false;
 
     // Other arguments
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
index 69f98b700..f62f12082 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
@@ -20,7 +20,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("ff02b1583ee3a12ed66a9c0e08e346b2")
+                Arrays.asList("45fef0e23113e2fcd9570379e2fc1b75")
         );
         executeTest("testBasicFunctionality", spec);
     }