diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 678a65024..4f18ece7b 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -423,16 +423,17 @@ public class GenotypingEngine {
     protected static VariantContext createMergedVariantContext( final VariantContext thisVC, final VariantContext nextVC, final byte[] ref, final GenomeLoc refLoc ) {
         final int thisStart = thisVC.getStart();
         final int nextStart = nextVC.getStart();
-        byte[] refBases = ( new byte[]{} );
-        byte[] altBases = ( new byte[]{} );
+        byte[] refBases = new byte[]{};
+        byte[] altBases = new byte[]{};
         refBases = ArrayUtils.addAll(refBases, thisVC.getReference().getBases());
         altBases = ArrayUtils.addAll(altBases, thisVC.getAlternateAllele(0).getBases());
-        for( int locus = thisStart + refBases.length; locus < nextStart; locus++ ) {
+        int locus;
+        for( locus = thisStart + refBases.length; locus < nextStart; locus++ ) {
             final byte refByte = ref[locus - refLoc.getStart()];
             refBases = ArrayUtils.add(refBases, refByte);
             altBases = ArrayUtils.add(altBases, refByte);
         }
-        refBases = ArrayUtils.addAll(refBases, nextVC.getReference().getBases());
+        refBases = ArrayUtils.addAll(refBases, ArrayUtils.subarray(nextVC.getReference().getBases(), locus > nextStart ? 1 : 0, nextVC.getReference().getBases().length)); // special case of deletion including the padding base of consecutive indel
         altBases = ArrayUtils.addAll(altBases, nextVC.getAlternateAllele(0).getBases());
 
         int iii = 0;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
index 4bcf5a0a0..539190fe9 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
@@ -353,6 +353,16 @@ public class GenotypingEngineUnitTest extends BaseTest {
         Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
         Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());
 
+        // deletion + insertion (abutting)
+        thisVC = new VariantContextBuilder().loc("2", 1701, 1702).alleles("AT","A").make();
+        nextVC = new VariantContextBuilder().loc("2", 1702, 1702).alleles("T","GCGCGC").make();
+        truthVC = new VariantContextBuilder().loc("2", 1701, 1702).alleles("AT","AGCGCGC").source("merged").make();
+        mergedVC = GenotypingEngine.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
+        logger.warn(truthVC + " == " + mergedVC);
+        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
+        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
+        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());
+
         // complex + complex
         thisVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("TC","AAA").make();
         nextVC = new VariantContextBuilder().loc("2", 1706, 1707).alleles("GG","AC").make();
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 9b8d1b3d7..9b149e8d1 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -30,10 +30,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
-        // TODO -- Ryan, do you know why the md5s changed just for the rank sum tests?
-        final String RyansMd5 = "ff370c42c8b09a29f1aeff5ac57c7ea6";
-        final String EricsMd5 = "d8317f4589e8e0c48bcd087cdb75ce88";
-        HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", EricsMd5);
+        HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "d8317f4589e8e0c48bcd087cdb75ce88");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -46,6 +43,5 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerMultiSampleComplex() {
         HCTestComplexVariants(CEUTRIO_BAM, "", "6f9fda3ea82c5696bed1d48ee90cd76b");
     }
-
 }