diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index 187df3c74..87f22ee96 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -184,7 +184,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         }
 
         record.setHeader(samHeaderMerger.getMergedHeader());
-        if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() > 0) {
+        if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() >= 0) {
             record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
         }