diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
index b1633edcb..52548dfa7 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
 import edu.mit.broad.picard.sam.SamFileHeaderMerger;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.iterators.BoundedReadIterator;
@@ -253,7 +254,6 @@ public class SAMDataSource implements SimpleDataSource {
                         this.readsAtLastPos = 1;
                     }
                     lastPos = rec.getAlignmentStart();
-                    //System.out.print("t" + rec.getAlignmentStart() + " ");
                     ++x;
                 } else {
                     // jump contigs
@@ -310,6 +310,16 @@ public class SAMDataSource implements SimpleDataSource {
         List<SAMFileReader> lst = new ArrayList<SAMFileReader>();
         for (File f : this.samFileList) {
             SAMFileReader reader = initializeSAMFile(f);
+
+            if (reader.getFileHeader().getReadGroups().size() < 1) {
+                logger.warn("Setting header in reader " + f.getName());
+                SAMReadGroupRecord rec = new   SAMReadGroupRecord(f.getName());
+                rec.setLibrary(f.getName());
+                rec.setSample(f.getName());
+
+                reader.getFileHeader().addReadGroup(rec);
+            }
+
             if (reader == null) {
                 throw new SimpleDataSourceLoadException("SAMDataSource: Unable to load file: " + f);
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
index 36cdb09aa..802423e5f 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
@@ -128,7 +128,6 @@ public class MicroManager {
                 walkerInitialized = true;
             }
 
-            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/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index 8dff73791..44145f562 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -16,10 +16,12 @@ import edu.mit.broad.picard.sam.SamFileHeaderMerger;
 import edu.mit.broad.picard.util.PeekableIterator;
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
+import org.apache.log4j.Logger;
 
 import java.lang.reflect.Constructor;
 import java.util.Comparator;
 import java.util.Iterator;
+import java.util.List;
 import java.util.PriorityQueue;
 
 /**
@@ -31,6 +33,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
     protected PriorityQueue<ComparableSamRecordIterator> pq = null;
     protected final SamFileHeaderMerger samHeaderMerger;
     protected final SAMFileHeader.SortOrder sortOrder;
+    protected static Logger logger = Logger.getLogger(MergingSamRecordIterator2.class);
 
     protected boolean initialized = false;
 
@@ -135,11 +138,20 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         if (oldProgramGroupId != null) {
             final String newProgramGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldProgramGroupId);
             record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
+        } else {
+            List<SAMReadGroupRecord> readGroups = iterator.getReader().getFileHeader().getReadGroups();
+            if (readGroups.size() == 1) {
+                record.setAttribute(SAMTag.RG.toString(), readGroups.get(0).getReadGroupId());
+                record.setAttribute(SAMTag.SM.toString(), readGroups.get(0).getReadGroupId());
+            } else {
+               logger.warn("Unable to set read group of ungrouped read: unable to pick default group, there are " + readGroups.size() + " possible.");
+            }
         }
 
         record.setHeader(samHeaderMerger.getMergedHeader());
         //System.out.printf("NEXT = %s %s %d%n", record.getReadName(), record.getReferenceName(), record.getAlignmentStart());
         //System.out.printf("PEEK = %s %s %d%n", this.pq.peek().peek().getReadName(), this.pq.peek().peek().getReferenceName(), this.pq.peek().peek().getAlignmentStart());
+
         return record;
     }