diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 363ec2412..94c3db651 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -264,7 +264,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
-                Arrays.asList("77bc144fd432b8886ab19ed20bfb9396"));
+                Arrays.asList("d0a381375a407dd454637f78bb5b194f"));
         executeTest("annotate a vcf with the FILTER field of another vcf", spec);
     }
 
@@ -354,7 +354,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testInbreedingCoeffPed() {
-        final String MD5 = "914e6882f01bae43f1d6ba1b0023cf91";
+        final String MD5 = "5cbf01dc895bff5a8dd9f6c46e0958c6";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
index 153b5ffaa..0f7f9fb67 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
@@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
         //TODO the old MD5 is kept for the record.
         //TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach.
 //        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2");
-        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "6fcffeb383100c1a11f0f0bff0a6e426");
+        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "988d421354869ec3b17f90bad695757a");
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
index f69a353a0..e683b34b7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
@@ -63,7 +63,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","62ef94ffa0670c6467cf90b27cc59a5d");
+        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","1ad2b57af06e90679ce6476900d9cbbe");
     }
 
     @Test(enabled = true)
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
index 12d775bb5..79385a81f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
@@ -92,7 +92,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("75381df9490adf4206ebbfbe0f49226e"));
+                Arrays.asList("7fca7fe87afba84c1bece29ce7a402ef"));
 
         executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
     }
@@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("92cbf13fd3ca797c2cacccf12890f40d"));
+                Arrays.asList("343307f432d2026e3c4cc44f64aad06f"));
 
         executeTest(String.format("test indel calling, multiple technologies"), spec);
     }
@@ -140,7 +140,7 @@ 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("feef70172d1edf2f9782143c8bbbf1d0"));
+                Arrays.asList("8052ee2044f3c5687859aadee2fe2a75"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
index 857474b55..39bd498f2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
@@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("03e6cb2c81775b94c81af45560062705"));
+                Arrays.asList("0de8363482204fe2aedbe612782d1049"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -118,7 +118,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("710d308a32012911fc275042b612e3d0"));
+                Arrays.asList("e86ff5eb488f29aa77606309b2fd4fcb"));
         executeTest("test reverse trim", spec);
     }
 
@@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("55f9bd98155a7a4b768fba97f90de282"));
+                Arrays.asList("d8b205bce4addb4ceff0b5a7ec36e3fe"));
         executeTest("test mismatched PLs", spec);
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index cfa6da336..9d09dd253 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex1() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6be5c8cbedea0a571c98fb1f4718042f");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "39a1dfa5143e04f75ecd2b24f9c69578");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 21b3ba5f9..e02ea56b6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -106,7 +106,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeBAMOutFlags() throws IOException {
-        HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "1ad8934dc0ea624ffeb89d3e877176b2", "f84c8bc44b6af548bd3b8555a068b59e");
+        HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "1ad8934dc0ea624ffeb89d3e877176b2", "6a81bbefa6c4ed7a6b8d2c3e0e5a4756");
     }
 
     @Test
@@ -296,7 +296,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testLeftAlignmentBamOutBugFix() {
         final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
                 + " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c1840293b4565ce1cef393c6a0d5fc9a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("01deba68f7a7d562b0e466f6858d42e3"));
         executeTest("LeftAlignmentBamOutBugFix", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index ae22d6ad5..9dfc49913 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -87,7 +87,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("27c0e81c71f599685f6bdc433652645d"));
+                Arrays.asList("39d4f9b5650667491091ccee7c245b06"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -127,7 +127,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("acfcca2d271c3403dc42a16e0494f11b"));
+                Arrays.asList("f06edaabb82af64f1465dd27b9c9948e"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 
@@ -137,7 +137,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
                         + " -L chr20:332341-802503",
                 1,
-                Arrays.asList("504e9af1f767db3d9da9bb6665daabcb"));
+                Arrays.asList("16ac184f0f8c81c9b4a6cbc235a58872"));
         executeTest("Use trio-phased VCF, adding read-backed phasing information in HP tag (as is now standard for RBP) [TEST SEVEN]", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
index 5e342f3b6..d28b5f708 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
@@ -226,7 +226,7 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
 
         // test pairs of strats
         new StratifiedEvalTestProvider(12,
-                Arrays.asList(4, 3, 2, 3),
+                Arrays.asList(3, 4, 3, 2),
                 Arrays.asList(1, 2), Arrays.asList(3, 4));
 
         return StratifiedEvalTestProvider.getTests(StratifiedEvalTestProvider.class);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 3a84e65fe..f94dbca8e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -196,7 +196,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
             "3ad7f55fb3b072f373cbce0b32b66df4",  // tranches
-            "73489f9365e4884b2dd89477350a7fe0",  // recal file
+            "48c21792897bdbb9adcc64886d03c5d1",  // recal file
             "0bd2067f831e5388b790e7bb7f45d98f"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
index cbcb02d17..7f0888c53 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -144,7 +144,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9bdda937754e1407183406808f560723"); } // official project VCF files in tabix format
     @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "6344953a82a422115bd647ec1d696b94"); } // official project VCF files in tabix format
-    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c4b995405872b22ded76c0a9e183c52d"); }
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "51cf4543e46c8434e32c426f59507d1e"); }
 
     @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f9d1d7e6246f0ce9e493357d5b320323"); }
 
@@ -169,7 +169,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("8f8ba6d671f67386883c11873df3cf95"));
+                Arrays.asList("8b75e835ed19c06c358a2185cd0e14db"));
         cvExecuteTest("threeWayWithRefs", spec, true);
     }
 
@@ -186,10 +186,10 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true);
     }
 
-    @Test public void complexTestFull() { combineComplexSites("", "3a702773e31674b14a1073d455f6f1ce"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "cabad0e328f1c967d44aaf2085da5dcf"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "31f6f62664cc5891e9a8e228dbb6278d"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "31f6f62664cc5891e9a8e228dbb6278d"); }
+    @Test public void complexTestFull() { combineComplexSites("", "80c3b7ba39c8a3f3511fc1ea61ecd4da"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "e7da95bbcf3890a4debbfa07cbd646e5"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d7ee8da6ceee4dd1212122c2e9cab2a6"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "d7ee8da6ceee4dd1212122c2e9cab2a6"); }
 
     @Test
     public void combineDBSNPDuplicateSites() {
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 91edcc02b..ee7396255 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -277,7 +277,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                         " --uniquifySamples", b37KGReference),
                 1,
-                Arrays.asList("b73f5bf5646695ca019d84d44c74c819"));
+                Arrays.asList("2492d55f0e688d01ef2d67f675c0e2d9"));
         executeTest("testUniquifiedSamples", spec);
 
     }
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
index 973d6cd44..df03b0b33 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
@@ -759,7 +759,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     public Object[][] getVCFFeaturesData() {
         return new Object[][]{
                 {"--sites_only", "6ef742ee6d9bcbc7b23f928c0e8a1d0e"},
-                {"--bcf", "285549ca1a719a09fa95cfa129520621"}
+                {"--bcf", "cdea454ac0af9e9228147f9c2ed1e0a6"}
         };
     }
 
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
index 475015939..62d358f1e 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
@@ -39,8 +39,8 @@ public class CramIntegrationTest extends WalkerTest {
     @DataProvider(name="cramData")
     public Object[][] getCRAMData() {
         return new Object[][] {
-                {"PrintReads", "exampleBAM.bam", "", "cram", "97470174cd313a4d200b2a96ffd73e99"},
-                {"PrintReads", "exampleCRAM.cram", "", "cram", "424c725c4ffe7215e358ecf5abd5e5e8"},
+                {"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name
+                {"PrintReads", "exampleCRAM.cram", "", "cram", ""},
                 {"PrintReads", "exampleCRAM.cram", "", "bam", "247805098718dd74b8a871796424d359"},
                 {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "a5b26631cd89f86f6184bcac7bc9c9ca"},
                 {"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
index e39f8aa5b..0f4789cfe 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
@@ -86,12 +86,12 @@ public class IntervalIntegrationTest extends WalkerTest {
                 Collections.<String>emptyList());
 
         // our base file
-        File baseOutputFile = createTempFile("testUnmappedReadInclusion", ".cram");
+        File baseOutputFile = createTempFile("testMultipleIntervalInclusionOnCRAM", ".cram");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("0f11cc035455cd68fb388e33aaf5feff", createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("", createTempFileFromBase(baseOutputFile.getAbsolutePath()));  // Bypass MD5 check since the CRAM header stores the file name
         spec.addAuxFile("ebbe6e311b6bb240554ec96ed9809216", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
 
-        executeTest("testUnmappedReadInclusionCRAM", spec);
+        executeTest("testMultipleIntervalInclusionOnCRAM", spec);
     }
 
     @Test
@@ -107,12 +107,12 @@ public class IntervalIntegrationTest extends WalkerTest {
                         Collections.<String>emptyList());
 
         // our base file
-        File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
+        File baseOutputFile = createTempFile("testMixedMappedAndUnmapped",".bam");
         spec.setOutputFileLocation(baseOutputFile);
         spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
-        executeTest("testUnmappedReadInclusion",spec);
+        executeTest("testMixedMappedAndUnmapped",spec);
     }
 
 
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index a6d5a8b37..e94b307be 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -44,8 +44,8 @@
         <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
 
         <!-- Version numbers for picard and htsjdk -->
-        <htsjdk.version>1.141</htsjdk.version>
-        <picard.version>1.141</picard.version>
+        <htsjdk.version>2.0.0</htsjdk.version>
+        <picard.version>2.0.0</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
index 1513fc5bf..40a571b8c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
@@ -92,14 +92,14 @@ public class CatVariantsIntegrationTest {
         final File catVariantsTempList2 = BaseTest.createTempListFile("CatVariantsTest2", CatVariantsVcf2.getAbsolutePath());
 
         new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
-        new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3");
+        new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "b7085b466ee49ba0857c6ff6ffe32bf3");
 
         for (String extension1 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
             for (String extension2 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
                 final File file1 = new File(CatVariantsDir, "CatVariantsTest1.vcf" + extension1);
                 final File file2 = new File(CatVariantsDir, "CatVariantsTest2.vcf" + extension2);
                 new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
-                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3");
+                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "820124f0ef22324e070ee21c91a633a4");
                 new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576");
             }
             new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576");
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
index 9b201b411..d064328c0 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
@@ -86,23 +86,23 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         // now add the expected files that get generated
         spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile);
         spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
-        spec.addAuxFile("520720a88ae7608257af51bc41c06b87", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
+        spec.addAuxFile("3bf1d7247ea68d1afb35c2032c68dbdf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
         spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
-        spec.addAuxFile("6958004a8156f3f267caa6b04cf90f5f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
-        spec.addAuxFile("ebbfc9b9f4e12ac989c127061948c565", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
-        spec.addAuxFile("e003bef6762833a5cebca25d94194616", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
+        spec.addAuxFile("681dcbedcf7ca14bb44134abd1d8da3f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
+        spec.addAuxFile("0f58e7f0909b84897fea5daebd9d2948", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
+        spec.addAuxFile("2832e48c12b1d8811ccd319a8ffb8dc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
         spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
-        spec.addAuxFile("0732b6d2db9c94b0fcf18ca1f19772a8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
+        spec.addAuxFile("22fee04ffca7fa489ae2e66309de12e4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
         spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
-        spec.addAuxFile("3522f7380554b926c71a7258250c1d63", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
-        spec.addAuxFile("2cd9d8c5e37584edd62ca6938659cf59", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
-        spec.addAuxFile("78fdd35a63a7a4c6b3a043b946b04730", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
+        spec.addAuxFile("2de22ad840bf40621e51316728a32fe9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
+        spec.addAuxFile("6c84a067016c63e8c2face2de800acc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
+        spec.addAuxFile("2629883b99428f51e2d90d820b45504a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
         spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
-        spec.addAuxFile("aa00e3652dd518ccbae2caa00171835b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
+        spec.addAuxFile("f6e52c5659f53afdcfc69c25272b9e99", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
         spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
-        spec.addAuxFile("0ce5ebfa46b081820d013bdbbfe42d34", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
-        spec.addAuxFile("c7c5bad6c6818995c634f350aa66fde9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
-        spec.addAuxFile("949c9ce745753cd98f337600d3931d09", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+        spec.addAuxFile("c2fb3a31d02df03c35afbe7f2284ad66", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("d1b3d08c6e9565a1dab727d089085761", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
+        spec.addAuxFile("c0fadfcfd88cec81ba0d57b33bdec277", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
 
         execute("testBaseOutputNoFiltering",spec);
     }
@@ -119,7 +119,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         spec.setOutputFileLocation(baseOutputFile);
 
         spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile);
-        spec.addAuxFile("4429d33ce8836c09ba2b5ddfae2f998e",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
+        spec.addAuxFile("fcaac186b7ccd10f3a6cb89ea49dcc1e",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
 
         execute("testNoCoverageDueToFiltering",spec);
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
index 0d9c7864a..a52059bb5 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
@@ -40,7 +40,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
         String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam "
                  + "-R " + hg18Reference
                  +  " -L chr15:46,347,148 -o %s";
-        String expected_md5 = "526c93b0fa660d6b953b57103e59fe98";
+        String expected_md5 = "22211a5da34a45b3b6045dbcbce8fede";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
         executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
     }
@@ -115,7 +115,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
                 + "-R " + hg18Reference
                 + " -outputInsertLength"
                 +  " -L chr15:46,347,148 -o %s";
-        String expected_md5 = "53ced173768f3d4d90b8a8206e72eae5";
+        String expected_md5 = "cae23b79598b23feec665704f5578897";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
         executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases (with insert length)", spec);
     }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
index 44c0bc2fe..17cc7c367 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
@@ -56,9 +56,9 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
 
     @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); }
-    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "906871df304dd966682e5798d59fc86b"); }
+    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); }
 
-    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "b41995fea04034ca0427c4a71504ef83"); }
+    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "b41995fea04034ca0427c4a71504ef83"); }
 
     @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
     @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
index 85d8c56ff..33684cda1 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -179,7 +179,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
         new MergeAllelesTest(Arrays.asList(ATref, ATC, Anoref, G),
                 Arrays.asList(Aref, ATCATC, G),
-                Arrays.asList(ATref, ATC, Anoref, G, ATCATCT, GT));
+                Arrays.asList(ATref, ATC, Anoref, G, GT, ATCATCT));
 
         return MergeAllelesTest.getTests(MergeAllelesTest.class);
     }