diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 74f803ac6..8334c99ec 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -236,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
+                            " -B:dbsnp " + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -L 1:10,000,000-10,200,000" +
@@ -284,7 +284,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
+                            " -B:anyNameABCD " + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -B:dbsnp,vcf " + b36dbSNP129 +
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 6bbaa266d..401fecb44 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -233,8 +233,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         String extraArgs = "-L 1:1-10,000,000";
         String tests = cmdRoot +
                 " -B:dbsnp " + b36dbSNP129 +
-                " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
-                " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
+                " -B:eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
+                " -B:comp_genotypes " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
                 1, Arrays.asList("14054badcd89b24c2375e1d09918f681"));
         executeTestParallel("testSelect1", spec);
@@ -244,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     public void testVEGenotypeConcordance() {
         String vcfFile = "GenotypeConcordanceEval.vcf";
 
-        WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
+        WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval " + validationDataLocation + vcfFile + " -B:comp " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
                 1,
                 Arrays.asList("96f27163f16bb945f19c6623cd6db34e"));
         executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
@@ -252,7 +252,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 
     @Test
     public void testCompVsEvalAC() {
-        String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
+        String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
         executeTestParallel("testCompVsEvalAC",spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
index 7cdb6af95..9655b514a 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
@@ -16,7 +16,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
 
     private static String root = cmdRoot +
             " -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 +
-            " -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
+            " -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
 
     private static final class VCITTest extends TestDataProvider {
         String args, md5;
@@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
     public void testToVCF() {
         // this really just tests that we are seeing the same number of objects over all of chr1
 
-        WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
+        WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
                 2, // just one output file
                 Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63"));
          executeTest("testToVCF", spec);