diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 898852211..004a98b10 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -486,4 +486,5 @@ public class GenomeAnalysisTK extends CommandLineProgram {
     }
 
     public SAMFileReader getSamReader() { return this.engine.getSamReader(); }
+    public TraversalEngine getEngine() { return this.engine; }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
index 133b9c4c3..26a817441 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
@@ -119,6 +119,9 @@ public class MicroManager {
             ReferenceProvider referenceProvider = new ReferenceProvider( refIter );
             LocusContextProvider locusProvider = new LocusContextProvider( readShard );
 
+            // set the sam header of the traversal engine
+            traversalEngine.setSAMHeader(readShard.getMergedHeader());
+            System.err.println(traversalEngine.getSAMHeader().getSequenceDictionary().toString());
             accumulator = traversalEngine.traverse( walker, shard, referenceProvider, locusProvider, accumulator );
             readShard.close();
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 479f267b0..7343a4d07 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -75,6 +75,11 @@ public abstract class TraversalEngine {
     protected boolean THREADED_IO = false;
     protected int THREADED_IO_BUFFER_SIZE = 10000;
 
+
+
+    // the stored header
+    protected SAMFileHeader myHeader = null;
+
     /**
      * our log, which we want to capture anything from this class
      */
@@ -168,6 +173,26 @@ public abstract class TraversalEngine {
     //
     // --------------------------------------------------------------------------------------------------------------
 
+
+    /**
+     * get the associated SAM header for our run
+     * @return the header if it's stored, null if not
+     */
+    public SAMFileHeader getSAMHeader() {
+        return myHeader;
+    }
+
+    /**
+     * set's the SAM header for this traversal, which should
+     * be the merged header in the multiple BAM file case.
+     *  
+     * @param myHeader the passed in header
+     */
+
+    public void setSAMHeader(SAMFileHeader myHeader) {
+        this.myHeader = myHeader;
+    }
+
     /**
      * Parses the location string locStr and sets the traversal engine to only process
      * regions specified by the location string.  The string is of the form:
@@ -417,7 +442,7 @@ public abstract class TraversalEngine {
 
     public boolean shutdown() {
         // todo: actually shutdown the resources
-        
+
         return true;
     }
 
@@ -462,7 +487,7 @@ public abstract class TraversalEngine {
     public <M, T> T traverse(Walker<M, T> walker, ArrayList<GenomeLoc> locations) {
         return null;
     }
-    
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // traversal by loci functions
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java
index 96df06062..a84ed8f80 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java
@@ -1,28 +1,21 @@
 
 package org.broadinstitute.sting.playground.gatk.walkers;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.gatk.*;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.refdata.rodGFF;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
+import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
-import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
 
-import java.util.*;
+import java.util.List;
 
 public class ListSampleIds extends LocusWalker<Boolean, Boolean> 
 {
     public void initialize() 
     { 
         GenomeAnalysisTK toolkit = this.getToolkit();
-        SAMFileHeader header = toolkit.getSamReader().getFileHeader();
+        SAMFileHeader header = toolkit.getEngine().getSAMHeader();
         List<SAMReadGroupRecord> read_groups = header.getReadGroups();
 
         for (int i = 0; i < read_groups.size(); i++)