diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
index 5c54252d7..0d9b8628c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
@@ -204,8 +204,10 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     // No testing of MD5 here, we previously blew up due to a 0 length haplotypes, so we just need to pass
     @Test
     public void testHaplotype0Length() {
+        final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper --disableDithering -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference + " -baq CALCULATE_AS_NECESSARY -glm BOTH -o /dev/null",
+                "-T UnifiedGenotyper --disableDithering -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference +
+                        " -baq CALCULATE_AS_NECESSARY -glm BOTH -o " + outputVCF,
                 0,
                 Collections.<String>emptyList());
         executeTest("testHaplotype0Length", spec);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index f7dde74c5..59f77e3c9 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -297,7 +297,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDoesNotFailOnBadRefBase() {
         // don't care about the output - just want to make sure it doesn't fail
-        final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2";
+        final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
+        final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o " + outputVCF + " -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.<String>emptyList());
         executeTest("HCTestDoesNotFailOnBadRefBase: ", spec);
     }
@@ -328,9 +329,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testLeftAlignmentBamOutBugFix() throws FileNotFoundException {
+        final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
         final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3";
         final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
-                + " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
+                + " --no_cmdline_in_header -bamout %s -o " + outputVCF  + " -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
         final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(md5BAMOut));
         executeTest("LeftAlignmentBamOutBugFix", spec);
         validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(LEFT_ALIGNMENT_BAMOUT_TEST_INPUT))), md5BAMOut);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
index d1bf66c97..3cc756cdb 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
@@ -84,9 +84,11 @@ public class HaplotypeCallerModesIntegrationTest extends WalkerTest {
     }
 
     public void HCTestBamWriter(final HaplotypeBAMWriter.Type type, final String md5) {
+        final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o /dev/null " +
-                        "-bamout %s -L 20:10,000,000-10,010,000 -bamWriterType " + type, 1,
+                "-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference +
+                        " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o " + outputVCF +
+                        " -bamout %s -L 20:10,000,000-10,010,000 -bamWriterType " + type, 1,
                 Arrays.asList(md5));
         executeTest("HC writing bams with mode " + type, spec);
     }
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index e6427dae5..96481ce57 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -44,8 +44,8 @@
         <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
 
         <!-- Version numbers for picard and htsjdk -->
-        <htsjdk.version>2.9.1</htsjdk.version>
-        <picard.version>2.9.0</picard.version>
+        <htsjdk.version>2.10.0</htsjdk.version>
+        <picard.version>2.9.2</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->