diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java
index 428b7355c..72b778ec9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import org.broad.tribble.util.BlockCompressedStreamConstants;
+import net.sf.samtools.util.BlockCompressedStreamConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.FileInputStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index 9cf0a9493..1cfb527cd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import org.broad.tribble.util.SeekableBufferedStream;
-import org.broad.tribble.util.SeekableFileStream;
+import net.sf.samtools.seekablestream.SeekableBufferedStream;
+import net.sf.samtools.seekablestream.SeekableFileStream;
 
 import net.sf.samtools.*;
 
diff --git a/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
index 11d152e65..a4ccd050a 100644
--- a/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
@@ -30,7 +30,7 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
-import org.broad.tribble.util.BlockCompressedInputStream;
+import net.sf.samtools.util.BlockCompressedInputStream;
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.variant.utils.GeneralUtils;
 import org.broadinstitute.variant.variantcontext.*;
diff --git a/public/packages/PicardPrivate.xml b/public/packages/PicardPrivate.xml
index a800294d6..d898a5d07 100644
--- a/public/packages/PicardPrivate.xml
+++ b/public/packages/PicardPrivate.xml
@@ -2,26 +2,9 @@
 <package name="picard-private-parts">
   <executable name="picard-private-parts">
     <dependencies>
-      <class name="edu.mit.broad.picard.genotype.DiploidGenotype" />
-      <class name="edu.mit.broad.picard.genotype.geli.GeliFileReader" />
-      <class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
-      <class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
-      <class name="edu.mit.broad.picard.util.PasteParser" />
       <class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
-      <class name="edu.mit.broad.picard.util.PicardFileSystemUtil" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
-      <class name="edu.mit.broad.picard.variation.VariantType" />
-      <class name="edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1" />
-      <class name="edu.mit.broad.picard.variation.AbstractKnownVariantCodec" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantIterator" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantCodecFactory" />
-      <class name="edu.mit.broad.picard.variation.KnownVariant" />
-      <class name="net.sf.picard.util.IlluminaUtil" />
       <class name="edu.mit.broad.picard.genotype.fingerprint.v2.FingerprintingSummaryMetrics" />
       <class name="edu.mit.broad.picard.genotype.concordance.DbSnpMatchMetrics" />
     </dependencies>
-
   </executable>
 </package>
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2375.jar b/settings/repository/edu.mit.broad/picard-private-parts-2375.jar
deleted file mode 100644
index bfa2f65ad..000000000
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-2375.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2662.jar b/settings/repository/edu.mit.broad/picard-private-parts-2662.jar
new file mode 100644
index 000000000..54ef6d5e2
Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-2662.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2375.xml b/settings/repository/edu.mit.broad/picard-private-parts-2662.xml
similarity index 58%
rename from settings/repository/edu.mit.broad/picard-private-parts-2375.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-2662.xml
index b467f934a..119255e8d 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-2375.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-2662.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2375" status="integration" publication="20120502094400" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2662" status="integration" publication="" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.67.1197.xml b/settings/repository/net.sf/picard-1.67.1197.xml
deleted file mode 100644
index 7d9042d6b..000000000
--- a/settings/repository/net.sf/picard-1.67.1197.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.67.1197" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.67.1197.jar b/settings/repository/net.sf/picard-1.84.1337.jar
similarity index 61%
rename from settings/repository/net.sf/picard-1.67.1197.jar
rename to settings/repository/net.sf/picard-1.84.1337.jar
index 9243c02df..68db41848 100644
Binary files a/settings/repository/net.sf/picard-1.67.1197.jar and b/settings/repository/net.sf/picard-1.84.1337.jar differ
diff --git a/settings/repository/net.sf/picard-1.84.1337.xml b/settings/repository/net.sf/picard-1.84.1337.xml
new file mode 100644
index 000000000..99f746ff6
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.84.1337.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.84.1337" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.67.1197.xml b/settings/repository/net.sf/sam-1.67.1197.xml
deleted file mode 100644
index d43aba4ed..000000000
--- a/settings/repository/net.sf/sam-1.67.1197.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.67.1197" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.67.1197.jar b/settings/repository/net.sf/sam-1.84.1337.jar
similarity index 67%
rename from settings/repository/net.sf/sam-1.67.1197.jar
rename to settings/repository/net.sf/sam-1.84.1337.jar
index 8a8343cfa..3d28e1928 100644
Binary files a/settings/repository/net.sf/sam-1.67.1197.jar and b/settings/repository/net.sf/sam-1.84.1337.jar differ
diff --git a/settings/repository/net.sf/sam-1.84.1337.xml b/settings/repository/net.sf/sam-1.84.1337.xml
new file mode 100644
index 000000000..4d31fe250
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.84.1337.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.84.1337" status="release" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-119.jar b/settings/repository/org.broad/tribble-1.84.1337.jar
similarity index 51%
rename from settings/repository/org.broad/tribble-119.jar
rename to settings/repository/org.broad/tribble-1.84.1337.jar
index c74bea398..a4c336101 100644
Binary files a/settings/repository/org.broad/tribble-119.jar and b/settings/repository/org.broad/tribble-1.84.1337.jar differ
diff --git a/settings/repository/org.broad/tribble-1.84.1337.xml b/settings/repository/org.broad/tribble-1.84.1337.xml
new file mode 100644
index 000000000..f14af794e
--- /dev/null
+++ b/settings/repository/org.broad/tribble-1.84.1337.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="org.broad" module="tribble" revision="1.84.1337" status="integration" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-119.xml b/settings/repository/org.broad/tribble-119.xml
deleted file mode 100644
index 08037b20e..000000000
--- a/settings/repository/org.broad/tribble-119.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="119" status="integration" />
-</ivy-module>