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 93a015718..363f7a357 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
@@ -245,8 +245,13 @@ public class PairHMMIndelErrorModel {
                 }
             }
             else {
-                final int refWindowStart = ref.getWindow().getStart();
-                final int refWindowStop  = ref.getWindow().getStop();
+                // extra padding on candidate haplotypes to make sure reads are always strictly contained
+                // in them - a value of 1 will in theory do but we use a slightly higher one just for safety sake, mostly
+                // in case bases at edge of reads have lower quality.
+                final int trailingBases = 3;
+                final int extraOffset = Math.abs(eventLength);
+                final int refWindowStart = ref.getWindow().getStart()+(trailingBases+extraOffset);
+                final int refWindowStop  = ref.getWindow().getStop()-(trailingBases+extraOffset);
 
                 if (DEBUG) {
                     System.out.format("Read Name:%s, aln start:%d aln stop:%d orig cigar:%s\n",p.getRead().getReadName(), p.getRead().getAlignmentStart(), p.getRead().getAlignmentEnd(), p.getRead().getCigarString());
@@ -255,10 +260,10 @@ public class PairHMMIndelErrorModel {
                 GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
 
                 if (!read.isEmpty() && (read.getSoftEnd() > refWindowStop && read.getSoftStart() < refWindowStop))
-                    read = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, ref.getWindow().getStop());
+                    read = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, refWindowStop);
 
                 if (!read.isEmpty() && (read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart))
-                    read = ReadClipper.hardClipByReferenceCoordinatesLeftTail (read, ref.getWindow().getStart());
+                    read = ReadClipper.hardClipByReferenceCoordinatesLeftTail (read, refWindowStart);
 
                 if (read.isEmpty())
                     continue;
@@ -270,7 +275,6 @@ public class PairHMMIndelErrorModel {
                     continue;
 
                 // get bases of candidate haplotypes that overlap with reads
-                final int trailingBases = 3;
                 final long readStart = read.getSoftStart();
                 final long readEnd = read.getSoftEnd();
 
@@ -286,7 +290,6 @@ public class PairHMMIndelErrorModel {
                 final int numEndSoftClippedBases = softClips ? read.getSoftEnd()- read.getAlignmentEnd() : 0 ;
                 final byte [] unclippedReadBases = read.getReadBases();
                 final byte [] unclippedReadQuals = read.getBaseQualities();
-                final int extraOffset = Math.abs(eventLength);
 
                 /**
                  * Compute genomic locations that candidate haplotypes will span.
@@ -313,6 +316,7 @@ public class PairHMMIndelErrorModel {
                     startLocationInRefForHaplotypes = ref.getWindow().getStop();                                        // read starts after haplotype: read will have to be clipped completely;
                 }
 
+                // candidate haplotype cannot go beyond reference context
                 if (stopLocationInRefForHaplotypes > ref.getWindow().getStop()) {
                     stopLocationInRefForHaplotypes = ref.getWindow().getStop();                                         // check also if end of read will go beyond reference context
                 }
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 c33e89b99..52970d70d 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("54e13f696f56eb742bf449ad11d0dc5f"));
+                Arrays.asList("8d9b8f8a1479322961c840e461b6dba8"));
 
         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("e87f5c76661527ef7aa44e528fe19573"));
+                Arrays.asList("3d4d66cc253eac55f16e5b0a36f17d8d"));
         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 253467a76..d55a923dc 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
@@ -240,7 +240,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("d995b76adc3766889f7c2c88da14055c"));
+                Arrays.asList("31be725b2a7c15e9769391ad940c0587"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -259,7 +259,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("9669e1643d22d5ad047b3941aeefd6db"));
+                Arrays.asList("dcc5cec42730567982def16da4a7f286"));
 
         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 a35cb1ecc..8256a8496 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("e3efd1917192ea743ac1e9958aa0a98f"));
+                Arrays.asList("a6c224235c21b4af816b1512eb0624df"));
         executeTest("test MultiSample Pilot1", spec);
     }