diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index f826cc59c..a70ebcc5d 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -235,15 +235,22 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         final SAMRecord record = iterator.next();
         addIfNotEmpty(iterator);
 
+        // Fix the read group if needs be
         if (this.samHeaderMerger.hasReadGroupCollisions()) {
-            final String id = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
-            final String newId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), id);
-            record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newId);
+            final String oldGroupId = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
+            if (oldGroupId != null ) {
+                final String newGroupId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), oldGroupId);
+                record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newGroupId);
+                }
         }
-        final String oldProgramGroupId = (String) record.getAttribute(SAMTag.PG.toString());
-        if (oldProgramGroupId != null) {
-            final String newProgramGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldProgramGroupId);
-            record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
+
+        // Fix the program group if needs be
+        if (this.samHeaderMerger.hasProgramGroupCollisions()) {
+            final String oldGroupId = (String) record.getAttribute(ReservedTagConstants.PROGRAM_GROUP_ID);
+            if (oldGroupId != null ) {
+                final String newGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldGroupId);
+                record.setAttribute(ReservedTagConstants.PROGRAM_GROUP_ID, newGroupId);
+            }
         }
 
         // if we don't have a read group, set one correctly