diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 6b6f8ba87..598a1f9eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
@@ -308,11 +309,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         writerToUse = writer;
 
         if ( N_WAY_OUT != null ) {
+ //           Map<String,String> args = getToolkit().getArguments().walkerArgs;
+            boolean createIndex =  true;
+
+ //           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);
+                writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),SAMFileHeader.SortOrder.coordinate,true, createIndex);
             } else {
-                writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true);
+                writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true, createIndex);
             }
 
         }   else {
diff --git a/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
index 64b20a308..3718345a4 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
@@ -51,20 +51,21 @@ public class NWaySAMFileWriter implements SAMFileWriter {
     private boolean presorted ;
     GenomeAnalysisEngine toolkit;
 
-    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted) {
+    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
         this.presorted = presorted;
         this.toolkit = toolkit;
         writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
-        setupByReader(toolkit,in2out,order, presorted);
+        setupByReader(toolkit,in2out,order, presorted, indexOnTheFly);
     }
 
-    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted) {
+    public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly ) {
         this.presorted = presorted;
         this.toolkit = toolkit;
         writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
-        setupByReader(toolkit,ext,order, presorted);
+        setupByReader(toolkit,ext,order, presorted, indexOnTheFly);
     }
 
+
     /**
      * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved
      * from <code>toolkit</code>). The <code>in2out</code> map must contain an entry for each input filename and map it
@@ -72,7 +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) {
+    public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
 
         if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL");
         for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
@@ -87,7 +88,7 @@ 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);
+            addWriter(rid,outName, order, presorted, indexOnTheFly);
         }
 
     }
@@ -100,7 +101,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
      * @param toolkit
      * @param ext
      */
-    public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted) {
+    public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
         for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
 
             String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
@@ -118,16 +119,16 @@ 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);
+            addWriter(rid,outName, order, presorted, indexOnTheFly);
         }
 
     }
 
-    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted) {
+    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) {
         File f = new File(outName);
         SAMFileHeader header = toolkit.getSAMFileHeader(id).clone();
         header.setSortOrder(order);
-        SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, f);
+        SAMFileWriter sw = new SAMFileWriterFactory().setCreateIndex(indexOnTheFly).makeSAMOrBAMWriter(header, presorted, f);
         writerMap.put(id,sw);
     }