diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java b/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
index 0d97a3842..9be2862fe 100755
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
@@ -204,6 +204,6 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
      * @return A unique set of matches.
      */
     private Set<ArgumentMatch> getUniqueMatches() {
-        return new HashSet<ArgumentMatch>( argumentMatches.values() );
+        return new LinkedHashSet<ArgumentMatch>( argumentMatches.values() );
     }    
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
index 5035053c3..b5be80195 100755
--- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
@@ -14,7 +14,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
 
     private static String root = cmdRoot +
             " -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
-            " -B vcf,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
+            " -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
 
     static HashMap<String, String> expectations = new HashMap<String, String>();
     static {
@@ -46,7 +46,7 @@ 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 + " -B vcf,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
+        WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B:vcf,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", "f4db5f7346792b1155693722bc190f63"));
          executeTest("testToVCF", spec);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java
index a87813aa0..348501b1e 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java
@@ -24,7 +24,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
+                        " -B:variant,GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
                         " -T VariantsToVCF" +
                         " -L 1:10,000,000-11,000,000" +
                         " -sample NA123AB" +
@@ -41,7 +41,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
+                        " -B:variant,GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
                         " -T VariantsToVCF" +
                         " -L 1:10,000,000-11,000,000" +
                         " -sample NA123AB" +
@@ -58,7 +58,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " -B variant,HapMap," + validationDataLocation + "rawHapMap.yri.chr1.txt" +
+                        " -B:variant,HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
                         " -T VariantsToVCF" +
                         " -L 1:1-1,000,000" +
                         " -o %s",
@@ -74,7 +74,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " -B variant,VCF," + validationDataLocation + "complexExample.vcf4" +
+                        " -B:variant,VCF " + validationDataLocation + "complexExample.vcf4" +
                         " -T VariantsToVCF" +
                         " -o %s",
                 1, // just one output file
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 5af50fb86..953e1bf3f 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -14,7 +14,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("89b846266a0c565b9d2a7dbe793546aa"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
@@ -22,7 +22,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("14e546fa7e819faeda3227c842fa92e7"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
@@ -30,7 +30,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("b48199f9dc6f91c61418536151afa8fd"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
@@ -38,7 +38,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("dcc7c522c4178b4fd9a0e5439bcdaebc"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
@@ -46,7 +46,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("34d2831e7d843093a2cf47c1f4e5f0f0"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
@@ -54,7 +54,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("20b946924fffdf6700cd029424fb72b5"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
@@ -62,7 +62,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("133275d150a8100ba4dc756d17b23ef1"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
@@ -70,7 +70,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("120fc0d4af1d370f1b306700258464b9"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
@@ -78,7 +78,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
                 Arrays.asList("10c31f8ab903843538a7604ed1e5405c"));
         executeTest("test overwriting header", spec);
     }
@@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("a6ec667a656e7ba368de9dbae781eef3"));
         executeTest("not passing it any reads", spec);
     }
@@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("8b4c309fe4900b5c8ae720c649715c7d"));
         executeTest("getting DB tag with dbSNP", spec);
     }
@@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B compH3,VCF," + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
+                baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("ff6b3468f21b262de671e823349cbb3c"));
         executeTest("getting DB tag with HM3", spec);
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
index 0108efc8f..10a7b7caa 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
@@ -30,7 +30,7 @@ import org.junit.Test;
 import java.util.Arrays;
 
 public class CompareCallableLociWalkerIntegrationTest extends WalkerTest {
-    final static String commonArgs = "-R " + hg18Reference + " -T CompareCallableLoci -B comp1,Bed," + validationDataLocation + "1kg_slx.chr1_10mb.callable -B comp2,Bed," + validationDataLocation + "ga2_slx.chr1_10mb.callable -o %s";
+    final static String commonArgs = "-R " + hg18Reference + " -T CompareCallableLoci -B:comp1,Bed " + validationDataLocation + "1kg_slx.chr1_10mb.callable -B:comp2,Bed " + validationDataLocation + "ga2_slx.chr1_10mb.callable -o %s";
 
     @Test
     public void testCompareCallableLociWalker1() {
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
index 92829806c..ae6bbdd2c 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
@@ -16,13 +16,13 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         executeTest("testFastaReference", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -B:snpmask,dbsnp /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
                  1,
                  Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
         WalkerTestSpec spec4 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B snps,GeliText," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:snps,GeliText " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B:snpmask,dbsnp /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
                  1,
                  Arrays.asList("82705a88f6fc25880dd2331183531d9a"));
         executeTest("testFastaAlternateReferenceSnps", spec4);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index de970181f..dfa4299d7 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -15,7 +15,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("89b846266a0c565b9d2a7dbe793546aa"));
         executeTest("test no action", spec);
     }
@@ -23,7 +23,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -window 10 -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("46877eb3ec258e6b70d8fcacca1acb25"));
         executeTest("test clustered SNPs", spec);
     }
@@ -31,7 +31,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testMask() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("650504a58af863d9cef699087a7961aa"));
         executeTest("test mask", spec);
     }
@@ -39,7 +39,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("b0b9110aeff967dd87cd0ec273d20791"));
         executeTest("test filter #1", spec);
     }
@@ -47,7 +47,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("8405a7ef69792c239d903d13832a1ea7"));
         executeTest("test filter #2", spec);
     }
@@ -55,7 +55,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("8266b9eb2ba35d77ab1cecb395322f31"));
         executeTest("test filter with separate names #2", spec);
     }
@@ -63,7 +63,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypeFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("99d8a47623cba215ee7d803c514ef116"));
         executeTest("test genotype filter #1", spec);
     }
@@ -71,7 +71,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypeFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("c58ea74c32290c9b4e8ae3dd1d0250e1"));
         executeTest("test genotype filter #2", spec);
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 299155d6c..3ade9f186 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -31,7 +31,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testRealignerKnownsOnly() {
         String[] md5s = {"7084d4e543bc756730ab306768028530", "74652bd8240291293ec921f8ecfa1622"};
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
+                "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B:knownIndels,VCF " + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
                  2,
                  Arrays.asList(md5s));
         executeTest("test realigner known indels only", spec);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index ef96b0576..7fd66f15d 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -23,7 +23,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
         executeTest("test dbsnp", spec2);
 
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + b36KGReference + " -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
+                "-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
                  1,
                  Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96"));
         executeTest("test rods only", spec3);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java
index 9d26129cc..48413d941 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java
@@ -18,7 +18,7 @@ public class ValidatingPileupIntegrationTest extends WalkerTest {
                 "-T ValidatingPileup" +
                 " -I " + validationDataLocation + "MV1994.selected.bam" +
                 " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
-                " -B pileup,SAMPileup,"+ validationDataLocation + "MV1994.selected.pileup" +
+                " -B:pileup,SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" +
                 " -S SILENT -nt 8",0, Collections.<String>emptyList());
         executeTest("testEcoliThreaded",spec);
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 05db302b2..eb5c60d67 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -202,7 +202,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B dbsnp,VCF," + validationDataLocation + "vcfexample3.vcf" +
+                            " -B:dbsnp,VCF " + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -L 1:10,000,000-10,200,000" +
@@ -226,7 +226,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B anyNameABCD,VCF," + validationDataLocation + "vcfexample3.vcf" +
+                            " -B:anyNameABCD,VCF " + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
index 25861c632..1d353bdd8 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
@@ -9,7 +9,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
     @Test
     public void testProbes() {
         String testVCF = validationDataLocation + "complexExample.vcf4";
-        String testArgs = "-R " + b36KGReference + " -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s";
+        String testArgs = "-R " + b36KGReference + " -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B:input,VCF "+testVCF+" -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("71e717e1813791575231f884b51c0aa3"));
         executeTest("Test probes", spec);
@@ -21,7 +21,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
         String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
                 + b36KGReference + " -omitWindow -nameConvention "
                 + "-project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
-                "pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
+                "pickSeqIntegrationTest.interval_list -B:input,VCF "+testVCF+" -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("0ab37fe4db3fef345815c56e57e75cec"));
         executeTest("Test probes", spec);
@@ -35,7 +35,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
         String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
                 + b36KGReference + " -omitWindow -nameConvention "
                 + "-nmw 1 -project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
-	    "pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
+	    "pickSeqIntegrationTest.interval_list -B:input,VCF "+testVCF+" -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
 						 Arrays.asList("8f0bc8954069c659c203cbb53d4dbad2"));
         executeTest("Test probes", spec);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java
index 54109d1a2..b2416cf13 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java
@@ -9,7 +9,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest {
     @Test
     public void testSNPs() {
         String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
-        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s";
+        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
         WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("2dab4630f40b76c0762de83fcbb60d09"));
         executeTest("Test SNPs", spec);
@@ -19,7 +19,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest {
     // TODO- need to be reenabled when PED reader tracks gets updated to read indels correctly
     public void testIndels() {
         String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
-        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s";
+        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
         WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("fad2dd71550dec064d458c4aa83e4de9"));
         executeTest("Test Indels", spec);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index ba2919ef2..532fc174c 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -24,7 +24,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                     "-R " + b36KGReference +
                             " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
                             " -T GenerateVariantClusters" +
-                            " -B input,VCF," + vcf +
+                            " -B:input,VCF " + vcf +
                             " -L 1:1-100,000,000" +
                             " --ignore_filter GATK_STANDARD" +
                             " -an QD -an HRun -an SB" +
@@ -51,7 +51,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         "-R " + b36KGReference +
                                 " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
                                 " -T VariantRecalibrator" +
-                                " -B input,VCF," + vcf +
+                                " -B:input,VCF " + vcf +
                                 " -L 1:40,000,000-100,000,000" +
                                 " --ignore_filter GATK_STANDARD" +
                                 " --ignore_filter HARD_TO_VALIDATE" +
@@ -89,7 +89,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
                                 " -T ApplyVariantCuts" +
                                 " -L 1:40,000,000-100,000,000" +
-                                " -B input,VCF," + inputVCFFile +
+                                " -B:input,VCF " + inputVCFFile +
                                 " -o %s" +
                                 " -tranchesFile " + tranchesFile,
                         1, // just one output file
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index db0a3c98e..9d8fb97ee 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -45,7 +45,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     public void test1InOut(String file, String md5, String args) {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 baseTestString(" -priority v1 -B v1,VCF," + validationDataLocation + file + args),
+                 baseTestString(" -priority v1 -B:v1,VCF " + validationDataLocation + file + args),
                  1,
                  Arrays.asList(md5));
          executeTest("testInOut1--" + file, spec);
@@ -53,7 +53,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     public void combine2(String file1, String file2, String args, String md5) {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 baseTestString(" -priority v1,v2 -B v1,VCF," + validationDataLocation + file1 + " -B v2,VCF," + validationDataLocation + file2 + args),
+                 baseTestString(" -priority v1,v2 -B:v1,VCF " + validationDataLocation + file1 + " -B:v2,VCF " + validationDataLocation + file2 + args),
                  1,
                  Arrays.asList(md5));
          executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
@@ -78,10 +78,10 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     @Test public void threeWayWithRefs() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(" -B NA19240_BGI,VCF,"+validationDataLocation+"NA19240.BGI.RG.vcf" +
-                        " -B NA19240_ILLUMINA,VCF,"+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
-                        " -B NA19240_WUGSC,VCF,"+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
-                        " -B denovoInfo,VCF,"+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
+                baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
+                        " -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
+                        " -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
+                        " -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
                         " -setKey centerSet" +
                         " -variantMergeOptions UNION" +
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index 4f3fe5349..27e7a34c6 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testb36Tohg19() {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + b36KGReference + " -B variant,vcf," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
+                 "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
                  Arrays.asList("1637877892a019061e74eb3d9a9d100f"));
          executeTest("test b36 to hg19", spec);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 7acbd0a27..4bc3bd514 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
 
         WalkerTestSpec spec = new WalkerTestSpec(
-            baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
+            baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B:variant,VCF " + testfile),
             1,
             Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
         );
diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java
index 14411d19e..8e1438cbf 100644
--- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java
@@ -21,7 +21,7 @@ public class ValidateRODForReadsIntegrationTest extends WalkerTest {
     @Test
     public void testSimpleVCFPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B vcf,vcf," + vcfFile, 1,
+                baseTestString1KG() + " -B:vcf,vcf " + vcfFile, 1,
                 Arrays.asList("f7919e9dc156fb5d3ad0541666864ea5"));
         executeTest("testSimpleVCFPileup", spec);
     }
@@ -29,7 +29,7 @@ public class ValidateRODForReadsIntegrationTest extends WalkerTest {
     @Test
     public void testSimpleDbSNPPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B dbsnp,dbsnp," + dbSNPFile, 1,
+                baseTestString1KG() + " -B:dbsnp,dbsnp " + dbSNPFile, 1,
                 Arrays.asList("c63b8ef9291a450f0519c73ac9cae189"));
         executeTest("testSimpleDbSNPPileup", spec);
     }
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
index e6e0ead0d..4128a3f13 100755
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
@@ -37,10 +37,10 @@ public class BeagleIntegrationTest extends WalkerTest {
     public void testBeagleOutput() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T BeagleOutputToVCF -R " + hg19Reference + " " +
-                        "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
-                        "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
-                        "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
-                        "-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " +
+                        "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
+                        "-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
+                        "-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
+                        "-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
                         "-o %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
         executeTest("test BeagleOutputToVCF", spec);
     }
@@ -49,7 +49,7 @@ public class BeagleIntegrationTest extends WalkerTest {
     public void testBeagleInput() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T ProduceBeagleInput -R " + hg19Reference + " " +
-                        "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
+                        "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
                          "-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e"));
         executeTest("test BeagleInput", spec);
     }
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java
index 7b6236187..ff9b21852 100755
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java
@@ -15,8 +15,8 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
         String[] md5 = {"d19d6d1eb52fb09e7493653dc645d92a"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T GenomicAnnotator -R " + b36KGReference + " " +
-                "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " +
-                "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " +
+                "-B:variant,vcf /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " +
+                "-B:dbsnp,AnnotatorInputTable /humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " +
                 "-m " + //generate many records from one input record if necessary
                 "-o %s " +
                 "-BTI variant",
@@ -29,8 +29,8 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
         String[] md5WithDashSArg = {"94edacdaee0dd58508d35d4d6040e31b"};
         WalkerTestSpec specWithSArg = new WalkerTestSpec(
                 "-T GenomicAnnotator -R " + b36KGReference +
-                " -B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" +
-                " -B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt" +
+                " -B:variant,vcf /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" +
+                " -B:dbsnp,AnnotatorInputTable /humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt" +
                 " -m" + //generate many records from one input record if necessary
                 " -o %s" +
                 " -BTI variant" +
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
index 379bd6654..44654c828 100644
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
@@ -18,7 +18,7 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
     @Test
     public void testSimpleGeliPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B eval,GeliText," + validationDataLocation + "ROD_validation/chr1.geli", 1,
+                baseTestString1KG() + " -B:eval,GeliText " + validationDataLocation + "ROD_validation/chr1.geli", 1,
                 Arrays.asList("832efb29a6d4e8dbae374d3eeee17d9d"));
         executeTest("testSimpleGeliPileup", spec);
     }
@@ -26,7 +26,7 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
     @Test
     public void testSimpleVCFPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf", 1,
+                baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf", 1,
                 Arrays.asList("5d84c75746738833b6c9441d9d614553"));
         executeTest("testSimpleVCFPileup", spec);
     }
@@ -34,8 +34,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
     @Test
     public void testComplexVCFPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
-                " -B eval2,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4"
+                baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" +
+                " -B:eval2,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4"
                 , 1,
                 Arrays.asList("8d97cbc29f73a0027267858f961e6fe5"));
         executeTest("testComplexVCFPileup", spec);
@@ -44,8 +44,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
     @Test
     public void testBTIWithROD() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
-                " -B eval2,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" + " -BTI eval"
+                baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" +
+                " -B:eval2,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" + " -BTI eval"
                 , 1,
                 Arrays.asList("ccfc0389a3c614f7892dbe972543f0ec"));
         executeTest("testBTIWithROD", spec);
@@ -54,9 +54,9 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
     @Test
     public void testLargeComplexVCFPileup() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
-                " -B eval2,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
-                " -B eval3,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
+                baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" +
+                " -B:eval2,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
+                " -B:eval3,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
                 " -L 1 -L 2 -L 20"
                 , 1,
                 Arrays.asList("8805912af2c38ec8d1cbc8d82532725e"));
@@ -67,8 +67,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
     public void testBlockZippedVrsUnzippedVCF1() {
         final String vcfName = validationDataLocation + "bgzipped_vcfs/vcfexample.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString1KG() + " -B eval,VCF," + vcfName +
-                " -B eval2,VCF," + vcfName + ".gz" +
+                baseTestString1KG() + " -B:eval,VCF " + vcfName +
+                " -B:eval2,VCF " + vcfName + ".gz" +
                 " --PerLocusEqual"
                 , 1,
                 Arrays.asList("ab3da32eae65e8c15a9f4a787a190a37"));