diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
index 8b5455e50..ce35baf15 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
@@ -129,9 +129,8 @@ class PhasingUtils {
         List<String> mergedIDs = new ArrayList<String>();
         if ( vc1.hasID() ) mergedIDs.add(vc1.getID());
         if ( vc2.hasID() ) mergedIDs.add(vc2.getID());
-        String mergedID = Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
+        String mergedID = mergedIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
 
-        // TODO -- FIX ID
         VariantContext mergedVc = new VariantContext(mergedName, mergedID, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs);
 
         mergedAttribs = new HashMap<String, Object>(mergedVc.getAttributes());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 8cc0d8856..f2d870068 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -1126,9 +1126,11 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         private double negLog10PError;
         private Set<String> filters;
         private Map<String, Object> attributes;
+        private String id;
 
         public UnfinishedVariantContext(VariantContext vc) {
             this.name = vc.getSource();
+            this.id = vc.getID();
             this.contig = vc.getChr();
             this.start = vc.getStart();
             this.stop = vc.getEnd();
@@ -1140,7 +1142,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         }
 
         public VariantContext toVariantContext() {
-            return new VariantContext(name, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
+            return new VariantContext(name, id, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
         }
 
         public GenomeLoc getLocation() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
index 260543031..b8c628717 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
@@ -70,9 +70,6 @@ public class GenotypeCollection implements List<Genotype> {
         return new GenotypeCollection(nGenotypes, false);
     }
 
-    // todo -- differentiate between empty constructor and copy constructor
-    // todo -- create constructor (Genotype ... genotypes)
-
     public static final GenotypeCollection create(final ArrayList<Genotype> genotypes) {
         return genotypes == null ? NO_GENOTYPES : new GenotypeCollection(genotypes, false);
     }
@@ -82,7 +79,7 @@ public class GenotypeCollection implements List<Genotype> {
     }
 
     public static final GenotypeCollection copy(final GenotypeCollection toCopy) {
-        return create(toCopy.genotypes);
+        return create(new ArrayList<Genotype>(toCopy.genotypes));
     }
 
     public static final GenotypeCollection copy(final Collection<Genotype> toCopy) {