diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index d36ec3411..9e07b1112 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -87,7 +87,12 @@ public class GATKSAMRecord extends BAMRecord {
                 read.getMateAlignmentStart(),
                 read.getInferredInsertSize(),
                 null);
-        super.clearAttributes();
+        SAMReadGroupRecord samRG = read.getReadGroup();
+        clearAttributes();
+        if (samRG != null) {
+            GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
+            setReadGroup(rg);
+        }
     }
 
     public GATKSAMRecord(final SAMFileHeader header,
@@ -134,6 +139,21 @@ public class GATKSAMRecord extends BAMRecord {
         return mReadGroup;
     }
 
+    @Override
+    public int hashCode() {
+        return super.hashCode();
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+
+        if (!(o instanceof GATKSAMRecord)) return false;
+
+        // note that we do not consider the GATKSAMRecord internal state at all
+        return super.equals(o);
+    }
+
     /**
      * Efficient caching accessor that returns the GATK NGSPlatform of this read
      * @return
@@ -147,11 +167,9 @@ public class GATKSAMRecord extends BAMRecord {
         retrievedReadGroup = true;
     }
 
-    //
-    //
-    // Reduced read functions
-    //
-    //
+    ///////////////////////////////////////////////////////////////////////////////
+    // *** ReduceReads functions                                              ***//
+    ///////////////////////////////////////////////////////////////////////////////
 
     public byte[] getReducedReadCounts() {
         if ( ! retrievedReduceReadCounts ) {
@@ -170,6 +188,12 @@ public class GATKSAMRecord extends BAMRecord {
         return getReducedReadCounts()[i];
     }
 
+
+    ///////////////////////////////////////////////////////////////////////////////
+    // *** GATKSAMRecord specific methods                                     ***//
+    ///////////////////////////////////////////////////////////////////////////////
+
+
     /**
      * Checks whether an attribute has been set for the given key.
      *
@@ -223,28 +247,26 @@ public class GATKSAMRecord extends BAMRecord {
         return null;
     }
 
-    @Override
-    public int hashCode() {
-        return super.hashCode();
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) return true;
-
-        if (!(o instanceof GATKSAMRecord)) return false;
-
-        // note that we do not consider the GATKSAMRecord internal state at all
-        return super.equals(o);
-    }
-
+    /**
+     * Checks whether if the read has any bases.
+     *
+     * Empty reads can be dangerous as it may have no cigar strings, no read names and
+     * other missing attributes.
+     *
+     * @return true if the read has no bases
+     */
     public boolean isEmpty() {
         return this.getReadLength() == 0;
     }
 
+    /**
+     * Clears all attributes except ReadGroup of the read.
+     */
     public void simplify () {
         GATKSAMReadGroupRecord rg = getReadGroup();
         this.clearAttributes();
         setReadGroup(rg);
     }
+
+
 }