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 6279e0061..c2e69ee2d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -4,6 +4,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.ArrayList;
@@ -38,14 +39,30 @@ public class ActiveRegion implements HasGenomeLocation {
         fullExtentReferenceLoc = fullExtentReferenceLoc.union( genomeLocParser.createGenomeLoc( read ) );
         reads.add( read );
     }
+    
+    public void hardClipToActiveRegion() {
+        final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, activeRegionLoc.getStart(), activeRegionLoc.getStop() );
+        reads.clear();
+        reads.addAll(clippedReads);
+    }
 
     public ArrayList<GATKSAMRecord> getReads() { return reads; }
 
-    public byte[] getReference( final IndexedFastaSequenceFile referenceReader ) {
-        return getReference( referenceReader, 0 );
+    public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader ) {
+        return getActiveRegionReference(referenceReader, 0);
     }
 
-    public byte[] getReference( final IndexedFastaSequenceFile referenceReader, final int padding ) {
+    public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader, final int padding ) {
+        return referenceReader.getSubsequenceAt( activeRegionLoc.getContig(),
+                Math.max(1, activeRegionLoc.getStart() - padding),
+                Math.min(referenceReader.getSequenceDictionary().getSequence(activeRegionLoc.getContig()).getSequenceLength(), activeRegionLoc.getStop() + padding) ).getBases();
+    }
+
+    public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader ) {
+        return getFullReference(referenceReader, 0);
+    }
+
+    public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader, final int padding ) {
        return referenceReader.getSubsequenceAt( fullExtentReferenceLoc.getContig(),
                Math.max(1, fullExtentReferenceLoc.getStart() - padding), 
                Math.min(referenceReader.getSequenceDictionary().getSequence(fullExtentReferenceLoc.getContig()).getSequenceLength(), fullExtentReferenceLoc.getStop() + padding) ).getBases();
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
index 7a664bd61..1eab43256 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
@@ -312,6 +312,42 @@ public class ReadClipper {
     }
 
 
+    /**
+     * Hard clip the read to the variable region (from refStart to refStop)
+     *
+     * @param read     the read to be clipped
+     * @param refStart the beginning of the variant region (inclusive)
+     * @param refStop  the end of the variant region (inclusive)
+     * @return the read hard clipped to the variant region
+     */
+    public static GATKSAMRecord hardClipToRegion( final GATKSAMRecord read, final int refStart, final int refStop ) {
+        final int start = read.getAlignmentStart();
+        final int stop = read.getAlignmentEnd();
+
+        // check if the read is contained in region
+        if (start <= refStop && stop >= refStart) {
+            if (start < refStart && stop > refStop)
+                return hardClipBothEndsByReferenceCoordinates(read, refStart - 1, refStop + 1);
+            else if (start < refStart)
+                return hardClipByReferenceCoordinatesLeftTail(read, refStart - 1);
+            else if (stop > refStop)
+                return hardClipByReferenceCoordinatesRightTail(read, refStop + 1);
+            return read;
+        } else
+            return GATKSAMRecord.emptyRead(read);
+
+    }
+    public static ArrayList<GATKSAMRecord> hardClipToRegion( final ArrayList<GATKSAMRecord> reads, final int refStart, final int refStop ) {
+        final ArrayList<GATKSAMRecord> returnList = new ArrayList<GATKSAMRecord>( reads.size() );
+        for( final GATKSAMRecord read : reads ) {
+            final GATKSAMRecord clippedRead = hardClipToRegion( read, refStart, refStop );
+            if( !clippedRead.isEmpty() ) {
+                returnList.add( clippedRead );
+            }
+        }
+        return returnList;
+    }
+
     /**
      * Checks if a read contains adaptor sequences. If it does, hard clips them out.
      *