diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
index 5b4a660e8..51993e1f2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
@@ -154,6 +154,13 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
     @Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "", required = false)
     protected boolean DONT_COMPRESS_READ_NAMES = false;
 
+    /**
+     * Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval
+     * border.
+     */
+    @Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "", required = false)
+    protected boolean HARD_CLIP_TO_INTERVAL = false;
+
     /**
      * Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be
      * considered consensus.
@@ -260,8 +267,14 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
             read = ReadClipper.hardClipAdaptorSequence(read);                                                           // Strip away adaptor sequences, if any.
         if (!DONT_CLIP_LOW_QUAL_TAILS)
             read = ReadClipper.hardClipLowQualEnds(read, minTailQuality);                                               // Clip low quality tails
-        if (!isWholeGenome())
-            mappedReads = hardClipReadToInterval(read);                                                                 // Hard clip the remainder of the read to the desired interval
+        if (!isWholeGenome()) {
+            if (HARD_CLIP_TO_INTERVAL)
+                mappedReads = hardClipReadToInterval(read);                                                             // Hard clip the remainder of the read to the desired interval
+            else {
+                mappedReads = new LinkedList<GATKSAMRecord>();
+                mappedReads.add(read);
+            }
+        }
         else {
             mappedReads = new LinkedList<GATKSAMRecord>();
             if (!read.isEmpty())
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
index f65d383e3..0a62afdc0 100755
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
@@ -21,28 +21,28 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testDefaultCompression() {
-        RRTest("testDefaultCompression ", L, "4c92d59d4a5292af1f968dc922c2c63e");
+        RRTest("testDefaultCompression ", L, "887d05e3bdbe831a2584305088806a39");
     }
 
     @Test(enabled = true)
     public void testMultipleIntervals() {
         String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
-        RRTest("testMultipleIntervals ", intervals, "97d5c3fda5551741676793ba325ec7ed");
+        RRTest("testMultipleIntervals ", intervals, "04208b8e2c2e65bcb9d0eb038702b006");
     }
 
     @Test(enabled = true)
     public void testHighCompression() {
-        RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "e6bc1cd0e9de961cf0fb1789bf6ab108");
+        RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "3a607bc3ebaf84e9dc44e005c5f8a047");
     }
 
     @Test(enabled = true)
     public void testLowCompression() {
-        RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "f33ec7cd0b98eebd73d1025ca656cd7e");
+        RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "afd39459c841b68a442abdd5ef5f8f27");
     }
 
     @Test(enabled = true)
     public void testIndelCompression() {
-        RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "e6e2bc889e4f342a7fedc5d38b391d20");
+        RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "f7b9fa44c10bc4b2247813d2b8dc1973");
     }
 
     @Test(enabled = true)
@@ -62,7 +62,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
     @Test(enabled = true)
     public void testAddingReadAfterTailingTheStash() {
         String base = String.format("-T ReduceReads %s -npt -R %s -I %s", STASH_L, REF, STASH_BAM) + " -o %s ";
-        executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("022931f032a4122cfe41e58e74d0aede")));
+        executeTest("testAddingReadAfterTailingTheStash", new WalkerTestSpec(base, Arrays.asList("886b43e1f26ff18425814dc7563931c6")));
     }
 }