diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index a273cf01d..0b0fa020e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -262,7 +262,7 @@ public class PairHMMIndelErrorModel {
      * @return true if the read needs to be clipped, false otherwise
      */
     protected static boolean mustClipDownstream(final GATKSAMRecord read, final int refWindowStop) {
-        return ( !read.isEmpty() && read.getSoftStart() < refWindowStop && read.getSoftStart() + read.getReadLength() > refWindowStop );
+        return ( !read.isEmpty() && read.getSoftStart() < refWindowStop && read.getSoftStart() + read.getReadLength() - 1 > refWindowStop );
     }
 
     /**
@@ -316,7 +316,7 @@ public class PairHMMIndelErrorModel {
 
                 // if the read extends beyond the downstream (right) end of the reference window, clip it
                 if ( mustClipDownstream(read, refWindowStop) )
-                    read = ReadClipper.hardClipByReadCoordinates(read, read.getSoftStart() + read.getReadLength() - refWindowStop + 1, read.getReadLength() - 1);
+                    read = ReadClipper.hardClipByReadCoordinates(read, refWindowStop - read.getSoftStart() + 1, read.getReadLength() - 1);
 
                 // if the read extends beyond the upstream (left) end of the reference window, clip it
                 if ( mustClipUpstream(read, refWindowStart) )
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
index 9556f9bf1..6219eb578 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
@@ -101,7 +101,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("3d12bdb816d27bf7c9efb4c13dc2aec7"));
+                Arrays.asList("e10c49fcf9a128745c2b050a52798e58"));
 
         executeTest(String.format("test indel calling, multiple technologies"), spec);
     }
@@ -136,7 +136,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
-                Arrays.asList("a2c8e83f37cd1e114b42af4b873f57bc"));
+                Arrays.asList("903af514f70db9238064da311c4ea0de"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 2cdddd49f..dcaed8bf2 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("150b31ba05113ca1996b548be5170d6d"));
+                Arrays.asList("c4248f02103e37e89b0f22c0d9c98492"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("7d0ee85cd89f4addd84c5511daaaa5c5"));
+                Arrays.asList("96c7862d55e933b274cabe45c9c443d9"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
index 18554e157..01aab8ae3 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
@@ -64,7 +64,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("ec0977e3fd3e2ac29c9821f0ca830455"));
+                Arrays.asList("710d379607129935b1b7b6960ca7b213"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java
index 38c06c25f..bbbef43d3 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java
@@ -130,4 +130,12 @@ public class PairHMMIndelErrorModelUnitTest extends BaseTest {
         final boolean result = PairHMMIndelErrorModel.mustClipDownstream(read, refWindowEnd);
         Assert.assertEquals(result, read.getSoftStart() < refWindowEnd && read.getSoftStart() + readLength > refWindowEnd);
     }
+
+    @Test
+    public void clipDownstreamAtBorderTest() {
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, 5, 10);
+        read.setCigarString("10M");
+        Assert.assertEquals(PairHMMIndelErrorModel.mustClipDownstream(read, 13), true);
+        Assert.assertEquals(PairHMMIndelErrorModel.mustClipDownstream(read, 14), false);
+    }
 }
\ No newline at end of file