diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index 5230381c0..11a59de10 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -94,6 +94,12 @@ public class ReadClipper {
         if (left == right)
             return new SAMRecord(read.getHeader());
         SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
+
+        // after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
+        // make the left cut index no longer part of the read. In that case, clip the read entirely.
+        if (left > leftTailRead.getAlignmentEnd())
+            return new SAMRecord(read.getHeader());
+
         ReadClipper clipper = new ReadClipper(leftTailRead);
         return clipper.hardClipByReferenceCoordinatesLeftTail(left);
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index a57154ff1..25f0d0fe2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -975,4 +975,5 @@ public class ReadUtils {
         AlignmentStartComparator comp = new AlignmentStartComparator();
         return comp.compare(read1, read2);
     }
+
 }