diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
index 90262b9c1..bae8e99ed 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
@@ -54,7 +54,8 @@ import java.util.*;
 public class FeatureManagerUnitTest extends BaseTest {
     private static final File RANDOM_FILE = new File(validationDataLocation + "exampleGATKReport.eval");
     private static final File VCF3_FILE = new File(validationDataLocation + "vcfexample3.vcf");
-    private static final File VCF4_FILE = new File(validationDataLocation + "vcf4.1.example.vcf");
+    private static final File VCF4_FILE = new File(testDir + "HiSeq.10000.vcf");
+    private static final File VCF4_FILE_GZ = new File(testDir + "HiSeq.10000.vcf.gz");
 
     private FeatureManager manager;
     private GenomeLocParser genomeLocParser;
@@ -98,7 +99,8 @@ public class FeatureManagerUnitTest extends BaseTest {
         }
 
         public String toString() {
-            return String.format("FMTest name=%s codec=%s feature=%s file=%s", name, codec, feature, associatedFile);
+            return String.format("FMTest name=%s codec=%s feature=%s file=%s",
+                    name, codec.getSimpleName(), feature.getSimpleName(), associatedFile);
         }
     }
 
@@ -106,6 +108,7 @@ public class FeatureManagerUnitTest extends BaseTest {
     public Object[][] createTests() {
         new FMTest(VariantContext.class, VCF3Codec.class, "VCF3", VCF3_FILE);
         new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE);
+        new FMTest(VariantContext.class, VCFCodec.class, "VCF", VCF4_FILE_GZ);
         new FMTest(TableFeature.class, BedTableCodec.class, "bedtable", null);
         return FMTest.getTests(FMTest.class);
     }
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 4abf0a102..3267173a7 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
@@ -38,21 +38,21 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
     }
 
-    public void test1InOut(String file, String md5, boolean vcf3) {
-        test1InOut(file, md5, "", vcf3);
+    public void test1InOut(String file, String md5) {
+        test1InOut(file, md5, "");
     }
 
-    public void test1InOut(String file, String md5, String args, boolean vcf3) {
+    public void test1InOut(String file, String md5, String args) {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 baseTestString(" -priority v1 -V:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
+                 baseTestString(" -priority v1 -V:v1 " + validationDataLocation + file + args),
                  1,
                  Arrays.asList(md5));
          executeTest("testInOut1--" + file, spec);
     }
 
-    public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
+    public void combine2(String file1, String file2, String args, String md5) {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 baseTestString(" -priority v1,v2 -V:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -V:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
+                 baseTestString(" -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 "+ validationDataLocation + file2 + args),
                  1,
                  Arrays.asList(md5));
          executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
@@ -78,23 +78,23 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
          executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
     }
 
-    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0", true); }
-    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo", true); }
-    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null", true); }
-    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0", false); } // official project VCF files in tabix format
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0"); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo"); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null"); }
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0"); } // official project VCF files in tabix format
 
-    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b", false); }
-    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e", false); }
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b"); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e"); }
 
     @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "0f873fed02aa99db5b140bcd6282c10a"); }
 
-    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
-    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
-    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a", false); }
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f"); } // official project VCF files in tabix format
+    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9"); } // official project VCF files in tabix format
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a"); }
 
-    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083", false); }
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083"); }
 
-    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
+    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c"); }
 
     @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4836086891f6cbdd40eebef3076d215a"); }
     @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "6a34b5d743efda8b2f3b639f3a2f5de8"); }