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 cea7dd007..8cf078e6e 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
@@ -744,62 +744,67 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
 
         String mvfLine;
 
-        if (tracker != null) {
-            VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
-            VariantContextBuilder builder = new VariantContextBuilder(vc);
+        if (tracker == null)
+            return metricsCounters;
 
-            GenotypesContext genotypesContext = GenotypesContext.copy(vc.getGenotypes());
-            for (Sample sample : trios) {
-                Genotype mother = vc.getGenotype(sample.getMaternalID());
-                Genotype father = vc.getGenotype(sample.getPaternalID());
-                Genotype child = vc.getGenotype(sample.getID());
+        final VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
+        if (vc == null)
+            return metricsCounters;
 
-                //Keep only trios and parent/child pairs
-                if(mother == null && father == null || child == null)
-                    continue;
+        final VariantContextBuilder builder = new VariantContextBuilder(vc);
 
-                ArrayList<Genotype> trioGenotypes = new ArrayList<Genotype>(3);
-                final int mvCount = phaseTrioGenotypes(vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), mother, father, child,trioGenotypes);
+        final GenotypesContext genotypesContext = GenotypesContext.copy(vc.getGenotypes());
+        for (Sample sample : trios) {
+            Genotype mother = vc.getGenotype(sample.getMaternalID());
+            Genotype father = vc.getGenotype(sample.getPaternalID());
+            Genotype child = vc.getGenotype(sample.getID());
 
-                Genotype phasedMother = trioGenotypes.get(0);
-                Genotype phasedFather = trioGenotypes.get(1);
-                Genotype phasedChild = trioGenotypes.get(2);
+            //Keep only trios and parent/child pairs
+            if(mother == null && father == null || child == null)
+                continue;
 
-                //Fill the genotype map with the new genotypes and increment metrics counters
-                genotypesContext.replace(phasedChild);
-                if(mother != null){
-                    genotypesContext.replace(phasedMother);
-                    if(father != null){
-                        genotypesContext.replace(phasedFather);
-                        updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters);
-                        mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
-                        if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
-                            metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
-                    }
-                    else{
-                        updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters);
-                        if(!(phasedMother.getType()==mother.getType() && phasedChild.getType()==child.getType()))
-                            metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
-                        mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
-                    }
+            ArrayList<Genotype> trioGenotypes = new ArrayList<Genotype>(3);
+            final int mvCount = phaseTrioGenotypes(vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), mother, father, child,trioGenotypes);
+
+            Genotype phasedMother = trioGenotypes.get(0);
+            Genotype phasedFather = trioGenotypes.get(1);
+            Genotype phasedChild = trioGenotypes.get(2);
+
+            //Fill the genotype map with the new genotypes and increment metrics counters
+            genotypesContext.replace(phasedChild);
+            if(mother != null){
+                genotypesContext.replace(phasedMother);
+                if(father != null){
+                    genotypesContext.replace(phasedFather);
+                    updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters);
+                    mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
+                    if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
+                        metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
                 }
                 else{
-                    genotypesContext.replace(phasedFather);
-                    updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters);
-                    if(!(phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
+                    updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters);
+                    if(!(phasedMother.getType()==mother.getType() && phasedChild.getType()==child.getType()))
                         metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
-                    mvfLine =   String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
+                    mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
                 }
-
-                //Report violation if set so
-                //TODO: ADAPT FOR PAIRS TOO!!
-                if(mvCount>0 && mvFile != null)
-                    mvFile.println(mvfLine);
+            }
+            else{
+                genotypesContext.replace(phasedFather);
+                updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters);
+                if(!(phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
+                    metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
+                mvfLine =   String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
             }
 
-            builder.genotypes(genotypesContext);
-            vcfWriter.add(builder.make());
+            //Report violation if set so
+            //TODO: ADAPT FOR PAIRS TOO!!
+            if(mvCount>0 && mvFile != null)
+                mvFile.println(mvfLine);
         }
+
+        builder.genotypes(genotypesContext);
+        vcfWriter.add(builder.make());
+
         return metricsCounters;
     }