diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index ba3154977..336cb3a65 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -789,6 +789,9 @@ public class VariantContextUtils {
 
             List<Allele> mergedAllelesForSample = new LinkedList<Allele>();
 
+            /* NOTE: Since merged alleles are added to mergedAllelesForSample in the SAME order as in the input VC records,
+               we preserve phase information (if any) relative to whatever precedes vc1:
+             */
             Iterator<Allele> all2It = site2Alleles.iterator();
             for (Allele all1 : site1Alleles) {
                 Allele all2 = all2It.next(); // this is OK, since allSamplesAreMergeable()
@@ -801,11 +804,11 @@ public class VariantContextUtils {
             Set<String> mergedGtFilters = new HashSet<String>(); // Since gt1 and gt2 were unfiltered, the Genotype remains unfiltered
 
             Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
-            Object PQ = gt1.getAttribute(ReadBackedPhasingWalker.PQ_KEY);
-            if (PQ != null)
-                mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, PQ);
+            PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
+            if (phaseQual.PQ != null)
+                mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);
 
-            Genotype mergedGt = new Genotype(sample, mergedAllelesForSample, mergedGQ, mergedGtFilters, mergedGtAttribs, calcPhaseForMergedGenotypes(gt1, gt2));
+            Genotype mergedGt = new Genotype(sample, mergedAllelesForSample, mergedGQ, mergedGtFilters, mergedGtAttribs, phaseQual.isPhased);
             mergedGenotypes.put(sample, mergedGt);
         }
 
@@ -1029,10 +1032,21 @@ public class VariantContextUtils {
         return (gt2.genotypesArePhased() || gt2.isHom() || gt1.isHom());
     }
 
+    private static class PhaseAndQuality {
+        public boolean isPhased;
+        public Double PQ = null;
+
+        public PhaseAndQuality(Genotype gt) {
+            this.isPhased = gt.genotypesArePhased();
+            if (this.isPhased)
+                this.PQ = VariantContextUtils.getDoubleAttribute(gt.getAttributes(), ReadBackedPhasingWalker.PQ_KEY);
+        }
+    }
+
     // Assumes that alleleSegregationIsKnown(gt1, gt2):
-    private static boolean calcPhaseForMergedGenotypes(Genotype gt1, Genotype gt2) {
+    private static PhaseAndQuality calcPhaseForMergedGenotypes(Genotype gt1, Genotype gt2) {
         if (gt2.genotypesArePhased() || gt2.isHom())
-            return gt1.genotypesArePhased(); // maintain the phase of gt1
+            return new PhaseAndQuality(gt1); // maintain the phase of gt1
 
         if (!gt1.isHom())
             throw new ReviewedStingException("alleleSegregationIsKnown(gt1, gt2) implies: gt2.genotypesArePhased() || gt2.isHom() || gt1.isHom()");
@@ -1048,7 +1062,7 @@ public class VariantContextUtils {
            0/1
            1/2
          */
-        return false; // maintain the phase of gt2 [since !gt2.genotypesArePhased()]
+        return new PhaseAndQuality(gt2); // maintain the phase of gt2 [since !gt2.genotypesArePhased()]
     }
 
     /* Checks if any sample has a MNP of ALT alleles (segregating together):
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index ad168399b..5d941ec17 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -28,6 +28,7 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -59,7 +60,8 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
     @Argument(fullName = "useSingleSample", shortName = "useSample", doc = "Only output genotypes for the single sample given; [default:use all samples]", required = false)
     protected String useSingleSample = null;
 
-    @Argument(fullName = "emitOnlyMergedRecords", shortName = "emitOnlyMerged", doc = "Only output records that resulted from merging; [default:false]", required = false)
+    @Hidden
+    @Argument(fullName = "emitOnlyMergedRecords", shortName = "emitOnlyMerged", doc = "Only output records that resulted from merging [For DEBUGGING purposes only - DO NOT USE, since it disregards the semantics of '|' as 'phased relative to previous non-filtered VC']; [default:false]", required = false)
     protected boolean emitOnlyMergedRecords = false;
 
     @Argument(fullName = "disablePrintAltAlleleStats", shortName = "noAlleleStats", doc = "Should the print-out of alternate allele statistics be disabled?; [default:false]", required = false)