diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 8680f3537..36e4db1c5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -248,6 +248,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     @Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file")
     protected String N_WAY_OUT = null;
 
+    @Hidden
+    @Argument(fullName="generate_nWayOut_md5s",doc="Generate md5sums for BAMs")
+    protected boolean generateMD5s = false;
 
     // DEBUGGING OPTIONS FOLLOW
 
@@ -401,9 +404,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
  //           if ( args.containsKey("disable_bam_indexing") )  { System.out.println("NO INDEXING!!"); System.exit(1); createIndex = false; }
 
             if ( N_WAY_OUT.toUpperCase().endsWith(".MAP") ) {
-                writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),SAMFileHeader.SortOrder.coordinate,true, createIndex);
+                writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),SAMFileHeader.SortOrder.coordinate,true, createIndex, generateMD5s);
             } else {
-                writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true, createIndex);
+                writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true, createIndex, generateMD5s);
             }
 
         }   else {
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
index 70417889b..07bfc52c7 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
@@ -51,18 +51,18 @@ public class NWaySAMFileWriter implements SAMFileWriter {
     private boolean presorted ;
     GenomeAnalysisEngine toolkit;
 
-    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
+    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
         this.presorted = presorted;
         this.toolkit = toolkit;
         writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
-        setupByReader(toolkit,in2out,order, presorted, indexOnTheFly);
+        setupByReader(toolkit,in2out,order, presorted, indexOnTheFly, generateMD5);
     }
 
-    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly ) {
+    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly , boolean generateMD5) {
         this.presorted = presorted;
         this.toolkit = toolkit;
         writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
-        setupByReader(toolkit,ext,order, presorted, indexOnTheFly);
+        setupByReader(toolkit,ext,order, presorted, indexOnTheFly, generateMD5);
     }
 
 
@@ -73,8 +73,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
      * @param toolkit
      * @param in2out
      */
-    public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
-
+    public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
         if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL");
         for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
 
@@ -88,7 +87,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
             if ( writerMap.containsKey( rid ) )
                 throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
 
-            addWriter(rid,outName, order, presorted, indexOnTheFly);
+            addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5);
         }
 
     }
@@ -101,7 +100,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
      * @param toolkit
      * @param ext
      */
-    public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
+    public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
         for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
 
             String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
@@ -119,16 +118,19 @@ public class NWaySAMFileWriter implements SAMFileWriter {
             if ( writerMap.containsKey( rid ) )
                 throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
 
-            addWriter(rid,outName, order, presorted, indexOnTheFly);
+            addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5);
         }
 
     }
 
-    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
+    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
         File f = new File(outName);
         SAMFileHeader header = toolkit.getSAMFileHeader(id).clone();
         header.setSortOrder(order);
-        SAMFileWriter sw = new SAMFileWriterFactory().setCreateIndex(indexOnTheFly).makeSAMOrBAMWriter(header, presorted, f);
+        SAMFileWriterFactory factory = new SAMFileWriterFactory();
+        factory.setCreateIndex(indexOnTheFly);
+        factory.setCreateMd5File(generateMD5);
+        SAMFileWriter sw = factory.makeSAMOrBAMWriter(header, presorted, f);
         writerMap.put(id,sw);
     }