diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
index 1d07215ad..5ef1f0cf0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
@@ -230,7 +230,7 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
         filterExps = VariantContextUtils.initializeMatchExps(FILTER_NAMES, FILTER_EXPS);
         genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
 
-        VariantContextUtils.engine.setSilent(true);
+        VariantContextUtils.engine.get().setSilent(true);
 
         initializeVcfWriter();
     }
diff --git a/settings/repository/net.sf/picard-1.102.1595.xml b/settings/repository/net.sf/picard-1.102.1595.xml
deleted file mode 100644
index e4370e4cd..000000000
--- a/settings/repository/net.sf/picard-1.102.1595.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.102.1595" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.102.1595.jar b/settings/repository/net.sf/picard-1.104.1628.jar
similarity index 91%
rename from settings/repository/net.sf/picard-1.102.1595.jar
rename to settings/repository/net.sf/picard-1.104.1628.jar
index 314b1db6a..0a24f339e 100644
Binary files a/settings/repository/net.sf/picard-1.102.1595.jar and b/settings/repository/net.sf/picard-1.104.1628.jar differ
diff --git a/settings/repository/net.sf/picard-1.104.1628.xml b/settings/repository/net.sf/picard-1.104.1628.xml
new file mode 100644
index 000000000..bd0c9fbcd
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.104.1628.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.104.1628" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.102.1595.xml b/settings/repository/net.sf/sam-1.102.1595.xml
deleted file mode 100644
index 44fc06d58..000000000
--- a/settings/repository/net.sf/sam-1.102.1595.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.102.1595" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.102.1595.jar b/settings/repository/net.sf/sam-1.104.1628.jar
similarity index 90%
rename from settings/repository/net.sf/sam-1.102.1595.jar
rename to settings/repository/net.sf/sam-1.104.1628.jar
index 23a464627..ad8437d03 100644
Binary files a/settings/repository/net.sf/sam-1.102.1595.jar and b/settings/repository/net.sf/sam-1.104.1628.jar differ
diff --git a/settings/repository/net.sf/sam-1.104.1628.xml b/settings/repository/net.sf/sam-1.104.1628.xml
new file mode 100644
index 000000000..0b0cba93f
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.104.1628.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.104.1628" status="release" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.102.1595.jar b/settings/repository/org.broad/tribble-1.104.1628.jar
similarity index 83%
rename from settings/repository/org.broad/tribble-1.102.1595.jar
rename to settings/repository/org.broad/tribble-1.104.1628.jar
index 4afeb3366..134be3d94 100644
Binary files a/settings/repository/org.broad/tribble-1.102.1595.jar and b/settings/repository/org.broad/tribble-1.104.1628.jar differ
diff --git a/settings/repository/org.broad/tribble-1.102.1595.xml b/settings/repository/org.broad/tribble-1.104.1628.xml
similarity index 75%
rename from settings/repository/org.broad/tribble-1.102.1595.xml
rename to settings/repository/org.broad/tribble-1.104.1628.xml
index 3500c3b08..c2158e974 100644
--- a/settings/repository/org.broad/tribble-1.102.1595.xml
+++ b/settings/repository/org.broad/tribble-1.104.1628.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.102.1595" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.104.1628" status="integration" />
 </ivy-module>
diff --git a/settings/repository/org.broadinstitute/variant-1.102.1595.jar b/settings/repository/org.broadinstitute/variant-1.104.1628.jar
similarity index 94%
rename from settings/repository/org.broadinstitute/variant-1.102.1595.jar
rename to settings/repository/org.broadinstitute/variant-1.104.1628.jar
index 18118bfae..59f4f10d7 100644
Binary files a/settings/repository/org.broadinstitute/variant-1.102.1595.jar and b/settings/repository/org.broadinstitute/variant-1.104.1628.jar differ
diff --git a/settings/repository/org.broadinstitute/variant-1.102.1595.xml b/settings/repository/org.broadinstitute/variant-1.104.1628.xml
similarity index 70%
rename from settings/repository/org.broadinstitute/variant-1.102.1595.xml
rename to settings/repository/org.broadinstitute/variant-1.104.1628.xml
index aa348fc84..527223bfb 100644
--- a/settings/repository/org.broadinstitute/variant-1.102.1595.xml
+++ b/settings/repository/org.broadinstitute/variant-1.104.1628.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.102.1595" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.104.1628" status="integration" />
 </ivy-module>