diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
index 49200911b..d1ba990fd 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
@@ -75,7 +75,7 @@ public class GATKVCFUtils {
         attributes.put("Date", date.toString());
         attributes.put("Epoch", Long.toString(date.getTime()));
         attributes.put("CommandLineOptions", engine.createApproximateCommandLineArgumentString(argumentSources.toArray()));
-        return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes, Collections.<String>emptyList());
+        return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes);
     }
 
     public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
diff --git a/settings/repository/net.sf/picard-1.96.1525.jar b/settings/repository/net.sf/picard-1.96.1534.jar
similarity index 95%
rename from settings/repository/net.sf/picard-1.96.1525.jar
rename to settings/repository/net.sf/picard-1.96.1534.jar
index 58bb179c3..8be3e01a3 100644
Binary files a/settings/repository/net.sf/picard-1.96.1525.jar and b/settings/repository/net.sf/picard-1.96.1534.jar differ
diff --git a/settings/repository/net.sf/picard-1.96.1525.xml b/settings/repository/net.sf/picard-1.96.1534.xml
similarity index 80%
rename from settings/repository/net.sf/picard-1.96.1525.xml
rename to settings/repository/net.sf/picard-1.96.1534.xml
index 6500aab1c..651193f22 100644
--- a/settings/repository/net.sf/picard-1.96.1525.xml
+++ b/settings/repository/net.sf/picard-1.96.1534.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.96.1525" status="release" />
+    <info organisation="net.sf" module="picard" revision="1.96.1534" status="release" />
 </ivy-module>
diff --git a/settings/repository/net.sf/sam-1.96.1525.xml b/settings/repository/net.sf/sam-1.96.1525.xml
deleted file mode 100644
index efc11ce6c..000000000
--- a/settings/repository/net.sf/sam-1.96.1525.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.96.1525" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.96.1525.jar b/settings/repository/net.sf/sam-1.96.1534.jar
old mode 100755
new mode 100644
similarity index 96%
rename from settings/repository/net.sf/sam-1.96.1525.jar
rename to settings/repository/net.sf/sam-1.96.1534.jar
index 73dd0ee48..474579754
Binary files a/settings/repository/net.sf/sam-1.96.1525.jar and b/settings/repository/net.sf/sam-1.96.1534.jar differ
diff --git a/settings/repository/net.sf/sam-1.96.1534.xml b/settings/repository/net.sf/sam-1.96.1534.xml
new file mode 100644
index 000000000..f72556cfb
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.96.1534.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.96.1534" status="release" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.96.1526.jar b/settings/repository/org.broad/tribble-1.96.1534.jar
similarity index 94%
rename from settings/repository/org.broad/tribble-1.96.1526.jar
rename to settings/repository/org.broad/tribble-1.96.1534.jar
index 0f45dbf52..c414565bf 100644
Binary files a/settings/repository/org.broad/tribble-1.96.1526.jar and b/settings/repository/org.broad/tribble-1.96.1534.jar differ
diff --git a/settings/repository/org.broad/tribble-1.96.1526.xml b/settings/repository/org.broad/tribble-1.96.1534.xml
similarity index 76%
rename from settings/repository/org.broad/tribble-1.96.1526.xml
rename to settings/repository/org.broad/tribble-1.96.1534.xml
index 6f3c52e1b..7bbb7d27b 100644
--- a/settings/repository/org.broad/tribble-1.96.1526.xml
+++ b/settings/repository/org.broad/tribble-1.96.1534.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.96.1526" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.96.1534" status="integration" />
 </ivy-module>
diff --git a/settings/repository/org.broadinstitute/variant-1.96.1525.jar b/settings/repository/org.broadinstitute/variant-1.96.1534.jar
similarity index 94%
rename from settings/repository/org.broadinstitute/variant-1.96.1525.jar
rename to settings/repository/org.broadinstitute/variant-1.96.1534.jar
index ffff1d4cc..1e34967fa 100644
Binary files a/settings/repository/org.broadinstitute/variant-1.96.1525.jar and b/settings/repository/org.broadinstitute/variant-1.96.1534.jar differ
diff --git a/settings/repository/org.broadinstitute/variant-1.96.1525.xml b/settings/repository/org.broadinstitute/variant-1.96.1534.xml
similarity index 71%
rename from settings/repository/org.broadinstitute/variant-1.96.1525.xml
rename to settings/repository/org.broadinstitute/variant-1.96.1534.xml
index eaa1d888f..0784e4891 100644
--- a/settings/repository/org.broadinstitute/variant-1.96.1525.xml
+++ b/settings/repository/org.broadinstitute/variant-1.96.1534.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.96.1525" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.96.1534" status="integration" />
 </ivy-module>