diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
index 7c956b855..18276f932 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -46,7 +46,7 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
     }
     
     public void hardClipToActiveRegion() {
-        final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, activeRegionLoc.getStart(), activeRegionLoc.getStop() );
+        final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, extendedLoc.getStart(), extendedLoc.getStop() );
         reads.clear();
         reads.addAll(clippedReads);
     }