diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
index a10a95e94..3b0a5eb4d 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
@@ -31,7 +31,6 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
@@ -51,17 +50,10 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
 
     private Logger logger;
 
-    private static class VCFRecord {
-        public VariantContext vc;
-        public byte refBase;
+    // Should we call innerWriter.close() in close()
+    private boolean takeOwnershipOfInner;
 
-        public VCFRecord(VariantContext vc, byte refBase) {
-            this.vc = vc;
-            this.refBase = refBase;
-        }
-    }
-
-    public MergePhasedSegregatingPolymorphismsToMNPvcfWriter(VCFWriter innerWriter, File referenceFile, int maxGenomicDistanceForMNP, Logger logger) {
+    public MergePhasedSegregatingPolymorphismsToMNPvcfWriter(VCFWriter innerWriter, File referenceFile, int maxGenomicDistanceForMNP, Logger logger, boolean takeOwnershipOfInner) {
         this.innerWriter = innerWriter;
         this.referenceFileForMNPmerging = new IndexedFastaSequenceFile(referenceFile);
         this.maxGenomicDistanceForMNP = maxGenomicDistanceForMNP;
@@ -69,6 +61,11 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
         this.filteredVcfrList = new LinkedList<VCFRecord>();
         this.numMergedRecords = 0;
         this.logger = logger;
+        this.takeOwnershipOfInner = takeOwnershipOfInner;
+    }
+
+    public MergePhasedSegregatingPolymorphismsToMNPvcfWriter(VCFWriter innerWriter, File referenceFile, int maxGenomicDistanceForMNP, Logger logger) {
+        this(innerWriter, referenceFile, maxGenomicDistanceForMNP, logger, false); // by default, don't own inner
     }
 
     public void writeHeader(VCFHeader header) {
@@ -76,13 +73,10 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
     }
 
     public void close() {
-        flush();
-        innerWriter.close();
-    }
-
-    public void flush() {
         stopWaitingToMerge();
-        innerWriter.flush();        
+
+        if (takeOwnershipOfInner)
+            innerWriter.close();
     }
 
     public void add(VariantContext vc, byte refBase) {
@@ -161,4 +155,14 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
     public String toString() {
         return getClass().getName();
     }
+
+    private static class VCFRecord {
+        public VariantContext vc;
+        public byte refBase;
+
+        public VCFRecord(VariantContext vc, byte refBase) {
+            this.vc = vc;
+            this.refBase = refBase;
+        }
+    }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
index 5bce26c80..4e54c3c2c 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
@@ -66,7 +66,8 @@ public class MergeSegregatingPolymorphismsWalker extends RodWalker<Integer, Inte
     }
 
     private void initializeVcfWriter() {
-        vcMergerWriter = new MergePhasedSegregatingPolymorphismsToMNPvcfWriter(writer, getToolkit().getArguments().referenceFile, maxGenomicDistanceForMNP, logger);
+        // false <-> don't take control of writer, since didn't create it:
+        vcMergerWriter = new MergePhasedSegregatingPolymorphismsToMNPvcfWriter(writer, getToolkit().getArguments().referenceFile, maxGenomicDistanceForMNP, logger, false);
         writer = null; // so it can't be accessed directly [i.e., not through vcMergerWriter]
 
         // setup the header fields:
@@ -132,7 +133,7 @@ public class MergeSegregatingPolymorphismsWalker extends RodWalker<Integer, Inte
      * @param result Empty for now...
      */
     public void onTraversalDone(Integer result) {
-        vcMergerWriter.flush();
+        vcMergerWriter.close();
         System.out.println("Number of records merged: " + vcMergerWriter.getNumMergedRecords());
     }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 852da9322..bcd286bde 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -124,8 +124,11 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     }
 
     private void initializeVcfWriter() {
+        // Wrapper VCFWriters will take ownership of inner writers iff: inner writer != origWriter [which wasn't created here]
+        VCFWriter origWriter = writer;
+
         if (enableMergePhasedSegregatingPolymorphismsToMNP)
-            writer = new MergePhasedSegregatingPolymorphismsToMNPvcfWriter(writer, getToolkit().getArguments().referenceFile, maxGenomicDistanceForMNP, logger);
+            writer = new MergePhasedSegregatingPolymorphismsToMNPvcfWriter(writer, getToolkit().getArguments().referenceFile, maxGenomicDistanceForMNP, logger, writer != origWriter);
 
         /* Due to discardIrrelevantPhasedSites(), the startDistance spanned by [partiallyPhasedSites.peek(), unphasedSiteQueue.peek()] is <= cacheWindow
            Due to processQueue(), the startDistance spanned by [unphasedSiteQueue.peek(), mostDownstreamLocusReached] is <= cacheWindow
@@ -136,7 +139,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
            But, NOTE that map() is careful to pass out a list of records to be written that FIRST includes any records discarded due to having reached mostDownstreamLocusReached,
            and only THEN records located at mostDownstreamLocusReached.  The opposite order in map() would violate the startDistance limits imposed when contracting SortingVCFWriter with (2 * cacheWindow).
          */
-        writer = new SortingVCFWriter(writer, 2 * cacheWindow);
+        writer = new SortingVCFWriter(writer, 2 * cacheWindow, writer != origWriter);
 
         // setup the header fields:
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@@ -923,7 +926,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     public void onTraversalDone(PhasingStats result) {
         List<VariantContext> finalList = processQueue(result, true); // process all remaining data
         writeVcList(finalList);
-        writer.flush();
+        writer.close();
 
         if (statsWriter != null)
             statsWriter.close();