diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index b308a6db6..9980d05a9 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -111,6 +111,9 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
 
     /** Returns true if any of the underlying iterators has more records, otherwise false. */
     public synchronized boolean hasNext() {
+        if (!initialized) {
+            lazyInitialization();
+        }
         return !this.pq.isEmpty();
     }