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 6d7c8dad9..d3a52167a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -261,7 +261,7 @@ public class GATKSAMRecord extends BAMRecord {
      * @return true if the read has no bases
      */
     public boolean isEmpty() {
-        return this.getReadLength() == 0;
+        return super.getReadBases() == null || super.getReadLength() == 0;
     }
 
     /**