diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index b83ef67c4..0b45dc931 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -16,7 +16,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("55785745fe13ad81a2c4a14373d091f0"));
+                Arrays.asList("360610e4990860bb5c45249b8ac31e5b"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("d6f749f8dbeb2d42c9effaff9fe571d7"));
+                Arrays.asList("d69a3c92a0e8f44e09e7377e3eaed4e8"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("9084e6c7b1cec0f3a2c6d96711844d5e"));
+                Arrays.asList("e0a08416249515ea18bd0663c90c9330"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("3dfabdcaa2648ac34380fb71860c42d3"));
+                Arrays.asList("0b60da46ba0eabb3abe5e0288937f9b0"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -48,7 +48,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b85c1ea28194484b327fbe0add1b5685"));
+                Arrays.asList("540a9be8a8cb85b0f675fea1184bf78c"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -58,7 +58,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         // they don't get reordered.  It's a good test of the genotype ordering system.
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("fe4d4e2484c4cf8b1cd50ad42cfe468e"));
+                Arrays.asList("f900e65b65ff0f9d9eb0891ef9b28c73"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("043fc6205b0633edcd3fadc9e044800c"));
+                Arrays.asList("5eb576d0234c912d8efea184492691d0"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("6fafb42d374a67ba4687a23078a126af"));
+                Arrays.asList("8860524d793d24b2e32f318433fcf527"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testExcludeAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("639462a0e0fa79e33def5f011fe55961"));
+                Arrays.asList("f33f417fad98c05d9cd08ffa22943b0f"));
         executeTest("test exclude annotations", spec);
     }
 
@@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("afe6c9d3b4b80635a541cdfcfa48db2f"));
+                Arrays.asList("1c423b7730b9805e7b885ece924286e0"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("21d696ea8c55d2fd4cbb4dcd5f7f7db6"));
+                Arrays.asList("54d7d5bb9404652857adf5e50d995f30"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
@@ -114,7 +114,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testMultipleIdsWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
-                Arrays.asList("ef95394c14d5c16682a322f3dfb9000c"));
+                Arrays.asList("5fe63e511061ed4f91d938e72e7e3c39"));
         executeTest("adding multiple IDs with dbSNP", spec);
     }
 
@@ -122,7 +122,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("e6e276b7d517d57626c8409589cd286f"));
+                Arrays.asList("cc7184263975595a6e2473d153227146"));
         executeTest("getting DB tag with HM3", spec);
     }
 
@@ -130,7 +130,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoQuals() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + privateTestDir + "noQual.vcf -A QualByDepth", 1,
-                Arrays.asList("a99e8315571ed1b6bce942451b3d8612"));
+                Arrays.asList("aea983adc01cd059193538cc30adc17d"));
         executeTest("test file doesn't have QUALs", spec);
     }
 
@@ -138,7 +138,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("7d6ea3b54210620cbc7e14dad8836bcb"));
+                Arrays.asList("2b0e8cdfd691779befc5ac123d1a1887"));
         executeTest("using expression", spec);
     }
 
@@ -146,13 +146,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("35ce4fb0288dfc5c01ec6ce8b14c6157"));
+                Arrays.asList("3de1d1998203518098ffae233f3e2352"));
         executeTest("using expression with ID", spec);
     }
 
     @Test
     public void testTabixAnnotations() {
-        final String MD5 = "5aebcf8f76c649d645708b1262185c80";
+        final String MD5 = "99938d1e197b8f10c408cac490a00a62";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
                     baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
@@ -168,7 +168,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile  " + validationDataLocation +
             "snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
             1,
-            Arrays.asList("0c20cda1cf0b903a287f1807ae5bee02")
+            Arrays.asList("d9291845ce5a8576898d293a829a05b7")
         );
         executeTest("Testing SnpEff annotations", spec);
     }
@@ -187,7 +187,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testTDTAnnotation() {
-        final String MD5 = "81f85f0ce8cc36df7c717c478e100ba1";
+        final String MD5 = "427dfdc665359b67eff210f909ebf8a2";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --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,
@@ -198,7 +198,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testChromosomeCountsPed() {
-        final String MD5 = "9830fe2247651377e68ad0b0894e9a4e";
+        final String MD5 = "6b5cbedf4a8b3385edf128d81c8a46f2";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --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,
@@ -208,7 +208,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testInbreedingCoeffPed() {
-        final String MD5 = "e94d589b5691e3ecfd9cc9475a384890";
+        final String MD5 = "159a771c1deaeffb786097e106943893";
         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/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
index 0458f2ad7..8fe96b53d 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
@@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                         "--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
                         "--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING", 1, Arrays.asList("cba514105039f7a56f7ecdd241fbdcca"));
+                        "-o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING", 1, Arrays.asList("c5522304abf0633041c7772dd7dafcea"));
         spec.disableShadowBCF();
         executeTest("test BeagleOutputToVCF", spec);
     }
@@ -75,7 +75,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
                 "--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
                 "--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
-                "-L 20:1-70000 -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",1,Arrays.asList("d95a97068a97c9059811b2574b73ea60"));
+                "-L 20:1-70000 -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",1,Arrays.asList("fbbbebfda35bab3f6f62eea2f0be1c01"));
         spec.disableShadowBCF();
         executeTest("testBeagleChangesSitesToRef",spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index 573f25b70..ae5128c75 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("fbf88e25df30181ca5422a374c7b36fa"));
+                Arrays.asList("a890cd298298e22bc04a2e5a20b71170"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("bb69f49e9ef0054f0ccd6d38f5ffa46a"));
+                Arrays.asList("f46b2fe2dbe6a423b5cfb10d74a4966d"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo --mask " + privateTestDir + "vcfexample2.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7e3225a32fcd6066901247992b2c5ca8"));
+                Arrays.asList("86dbbf62a0623b2dc5e8969c26d8cb28"));
         executeTest("test mask all", spec1);
     }
 
@@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("3485fe95e3f0864c3575baf05cef4bcc"));
+                Arrays.asList("2fb33fccda1eafeea7a2f8f9219baa39"));
         executeTest("test mask some", spec2);
     }
 
@@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask3() {
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("367ab9c028a68e4eda2055e3bb8b486c"));
+                Arrays.asList("4351e00bd9d821e37cded5a86100c973"));
         executeTest("test mask extend", spec3);
     }
 
@@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("5a10d969e50a58d8dfbf1da54bf293df"));
+                Arrays.asList("2f056b50a41c8e6ba7645ff4c777966d"));
         executeTest("test filter #1", spec);
     }
 
@@ -64,7 +64,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("886dbbca2350083819ff67224f6efbd6"));
+                Arrays.asList("b2a8c1a5d99505be79c03120e9d75f2f"));
         executeTest("test filter #2", spec);
     }
 
@@ -72,7 +72,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ee78c2e7128a8f9549233493c7cf6949"));
+                Arrays.asList("e350d9789bbdf334c1677506590d0798"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -80,7 +80,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("285dd348c47c8c1e85d2886f9b33559e"));
+                Arrays.asList("060e9e7b6faf8b2f7b3291594eb6b39c"));
         executeTest("test genotype filter #1", spec1);
     }
 
@@ -88,7 +88,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a9c835a13eb72aa22d5e271894d8ac33"));
+                Arrays.asList("00f90028a8c0d56772c47f039816b585"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -96,7 +96,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testDeletions() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + privateTestDir + "twoDeletions.vcf", 1,
-                Arrays.asList("a1c02a5a90f1262e9eb3d2cad1fd08f2"));
+                Arrays.asList("8077eb3bab5ff98f12085eb04176fdc9"));
         executeTest("test deletions", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
index b3c85622e..19d1e4cb3 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
@@ -29,7 +29,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("cd112ec37a9e28d366aff29a85fdcaa0","313cc749c7ee97713e4551de39e01ac5")
+                Arrays.asList("cd112ec37a9e28d366aff29a85fdcaa0","f8721f4f5d3bae2848ae15c3f120709b")
         );
         executeTest("testTrueNegativeMV", spec);
     }
@@ -48,7 +48,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("27ccd6feb51de7e7dcdf35f4697fa4eb","dd90dad9fd11e1b16e6660c3ca0553e7")
+                Arrays.asList("27ccd6feb51de7e7dcdf35f4697fa4eb","547fdfef393f3045a96d245ef6af8acb")
         );
         executeTest("testTruePositiveMV", spec);
     }
@@ -67,7 +67,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("719d681bb0a52a40bc854bba107c5c94","b35a86d2cad17f0db7b5e84ddc0e5545")
+                Arrays.asList("719d681bb0a52a40bc854bba107c5c94","9529e2bf214d72e792d93fbea22a3b91")
         );
         executeTest("testFalsePositiveMV", spec);
     }
@@ -86,7 +86,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("7f4a277aee2c7398fcfa84d6c98d5fb3","c53b5fd377bef48e9c6035a94db398db")
+                Arrays.asList("7f4a277aee2c7398fcfa84d6c98d5fb3","8c157d79dd00063d2932f0d2b96f53d8")
         );
         executeTest("testSpecialCases", spec);
     }
@@ -108,7 +108,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("44e09d2f9e4d8a9488226d03a97fe999","6f596470740e1a57679bbb38c0126364")
+                Arrays.asList("44e09d2f9e4d8a9488226d03a97fe999","343e418850ae4a687ebef2acd55fcb07")
         );
         executeTest("testPriorOption", spec);
     }
@@ -128,7 +128,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("b35a86d2cad17f0db7b5e84ddc0e5545")
+                Arrays.asList("9529e2bf214d72e792d93fbea22a3b91")
         );
         executeTest("testMVFileOption", spec);
     }
@@ -149,7 +149,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-fatherAlleleFirst"
                 ),
                 2,
-                Arrays.asList("60ced3d078792a150a03640b62926857","6d550784382aa910f78b533d889c91c0")
+                Arrays.asList("60ced3d078792a150a03640b62926857","52ffa82428e63ade22ea37b72ae58492")
         );
         executeTest("testFatherAlleleFirst", spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index bb4b7a1be..11f1a0628 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -26,7 +26,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("442c819569417c1b7d6be9f41ce05394"));
+                Arrays.asList("1c9a7fe4db41864cd85d16e5cf88986c"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -36,7 +36,7 @@ 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("2a51ee7d3c024f2410dcee40c5412993"));
+                Arrays.asList("a3ca151145379e0d4bae64a91165ea0b"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -46,7 +46,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("85bc9b03e24159f746dbd0cb988f9ec8"));
+                Arrays.asList("f685803333123a102ce1851d984cbd10"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -56,7 +56,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("96bb413a83c777ebbe622438e4565e8f"));
+                Arrays.asList("aaa7c25d118383639f273128d241e140"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -66,7 +66,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("7d2402f055d243e2208db9ea47973e13"));
+                Arrays.asList("418e29400762972e77bae4f73e16befe"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -76,7 +76,7 @@ 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("72682b3f27c33580d2d4515653ba6de7"));
+                Arrays.asList("4c8f6190ecc86766baba3aba08542991"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 0e213a090..8d6a18de0 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
             "0ddd1e0e483d2eaf56004615cea23ec7",  // tranches
             "b9709e4180e56abc691b208bd3e8626c",  // recal file
-            "c58ff4140e8914f0b656ed625c7f73b9"); // cut VCF
+            "4c73ff0c8c5ae0055bfacf33329a2406"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -119,6 +119,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -tranchesFile " + getMd5DB().getMD5FilePath(params.tranchesMD5, null) +
                         " -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null),
                 Arrays.asList(params.cutVCFMD5));
+        spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
         executeTest("testApplyRecalibrationIndel-"+params.inVCF, spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 2bd91ca85..bbee99ba6 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -142,17 +142,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
     }
 
-    @Test public void complexTestFull() { combineComplexSites("", "8b19b54516b59de40992f0c4b328258a"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "a38dd097adc37420fe36ef8be14cfded"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "a3957dac9a617f50ce2668607e3baef0"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "a3957dac9a617f50ce2668607e3baef0"); }
+    @Test public void complexTestFull() { combineComplexSites("", "151a4970367dd3e73ba3e7f3c2f874f6"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "c0625e092b878b3d3eb1703c48e216b7"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "6978329d6a1033ac16f83b49072c679b"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "6978329d6a1033ac16f83b49072c679b"); }
 
     @Test
     public void combineDBSNPDuplicateSites() {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
                  1,
-                 Arrays.asList("3d2a5a43db86e3f6217ed2a63251285b"));
+                 Arrays.asList("aa926eae333208dc1f41fe69dc95d7a6"));
          cvExecuteTest("combineDBSNPDuplicateSites:", spec);
     }
 }
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index 1711e6e3c..e14580ead 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("a139480c004859452d4095fe4859b42e"));
+                 Arrays.asList("7d5f91fcf419211ae9eca6c66dcec0e6"));
          executeTest("test b36 to hg19", spec);
     }
 
@@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("91344768f1e98c979364ec0d5d3aa9d6"));
+                 Arrays.asList("29dab3555e7f1ee6a60e267b00215a11"));
          executeTest("test b36 to hg19, unsorted samples", spec);
     }
 
@@ -58,7 +58,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + privateTestDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("e0b813ff873185ab51995a151f80ec98"));
+                 Arrays.asList("7e7bad0e1890753a01303c09a38ceb8d"));
          executeTest("test hg18 to hg19, unsorted", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 7af9a7aa3..30cdbee36 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -34,7 +34,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C --variant " + testfile),
                 1,
-                Arrays.asList("337bb7fc23153cf67acc42a466834775")
+                Arrays.asList("3d98a024bf3aecbd282843e0af89d0e6")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -64,7 +64,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
                 1,
-                Arrays.asList("ad0514b723ee1479d861291622bd4311")
+                Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b")
         );
         spec.disableShadowBCF();
         executeTest("testComplexSelection--" + testfile, spec);
@@ -78,7 +78,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
                 1,
-                Arrays.asList("bc0e00d0629b2bc6799e7e9db0dc775c")
+                Arrays.asList("1f5c72951a35667c4bdf1be153787e27")
         );
         spec.disableShadowBCF();
 
@@ -109,7 +109,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("a111642779b05de33ad04073d6022c21")
+                Arrays.asList("ca2b70e3171420b08b0a2659bfe2a794")
         );
 
         executeTest("testVariantTypeSelection--" + testFile, spec);
@@ -176,7 +176,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 2"),
                 1,
-                Arrays.asList("ad0514b723ee1479d861291622bd4311")
+                Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b")
         );
         spec.disableShadowBCF();
         executeTest("testParallelization (2 threads)--" + testfile, spec);
@@ -190,7 +190,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile + " -nt 4"),
                 1,
-                Arrays.asList("ad0514b723ee1479d861291622bd4311")
+                Arrays.asList("433eccaf1ac6e6be500ef0984a5d8d8b")
         );
         spec.disableShadowBCF();
 
@@ -204,7 +204,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
                 1,
-                Arrays.asList("9acd6effcc78bfb832bed5edfd6a1b5b")
+                Arrays.asList("3ab35d5e81a29fb5db3e2add11c7e823")
         );
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }
@@ -223,7 +223,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         final String testFile = privateTestDir + "missingHeaderLine.vcf";
         final String cmd = "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp "
                 + testFile + " -o %s --no_cmdline_in_header"
-                + (expectedException == null ? " -lenientVCFProcessing" : "");
+                + (expectedException == null ? " -U LENIENT_VCF_PROCESSING" : "");
         WalkerTestSpec spec =
                 expectedException != null
                         ? new WalkerTestSpec(cmd, 1, expectedException)
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
index eb79228e7..b0870b346 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
@@ -89,7 +89,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("95898aad8c9f9515c0e668e2fb65a024");
+        md5.add("21084d32ce7ac5df3cee1730bfaaf71c");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +