diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index a26b7134b..87375c843 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -146,13 +146,7 @@
                                     </includes>
                                 </filter>
                                 <filter>
-                                    <artifact>org.broad:tribble</artifact>
-                                    <includes>
-                                        <include>**</include>
-                                    </includes>
-                                </filter>
-                                <filter>
-                                    <artifact>org.broadinstitute:variant</artifact>
+                                    <artifact>samtools:htsjdk</artifact>
                                     <includes>
                                         <include>**</include>
                                     </includes>
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
index dc36e83c2..35388dc65 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java
index 463707252..d1e689d63 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java
index db52402a4..6d695f43c 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 /**
  * A temporary solution to work around Java access rights issues:
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
index 131793268..00f65e54c 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 /**
  * Utils that insist on being in the same package as Picard.
diff --git a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
index d03c6e006..aaa20c0e5 100644
--- a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
+++ b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
index 09a87d311..2b08fc4d4 100644
--- a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
+++ b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 9e06dce73..a8500815c 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -28,15 +28,10 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <!-- Tribble codecs -->
+        <!-- Tribble codecs & the variant package (VCF, BCF, and VariantContext) -->
         <dependency>
-            <groupId>org.broad</groupId>
-            <artifactId>tribble</artifactId>
-        </dependency>
-        <!-- The variant package (VCF, BCF, and VariantContext) -->
-        <dependency>
-            <groupId>org.broadinstitute</groupId>
-            <artifactId>variant</artifactId>
+            <groupId>samtools</groupId>
+            <artifactId>htsjdk</artifactId>
         </dependency>
         <!-- Workaround - depend on the logger impl required by JEXL -->
         <dependency>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index cb75a6891..3a266236c 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -44,7 +44,7 @@
         </dependency>
         <!-- Picard -->
         <dependency>
-            <groupId>net.sf</groupId>
+            <groupId>picard</groupId>
             <artifactId>picard</artifactId>
         </dependency>
         <!-- JavaMail -->
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index fe807da50..38078312f 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -42,12 +42,9 @@
         <java.gc.heapFreeLimit>10</java.gc.heapFreeLimit>
         <test.args>-Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit}</test.args>
 
-        <!-- Version numbers for picard sam-jdk. Usually kept in sync. -->
-        <picard.public.version>1.111.1920</picard.public.version>
-        <sam.version>${picard.public.version}</sam.version>
-        <picard.version>${picard.public.version}</picard.version>
-        <variant.version>${picard.public.version}</variant.version>
-        <tribble.version>${picard.public.version}</tribble.version>
+        <!-- Version numbers for picard and htsjdk -->
+        <htsjdk.version>1.112.1452</htsjdk.version>
+        <picard.version>1.112.1452</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
@@ -69,9 +66,9 @@
                 <version>1.0-r139</version>
             </dependency>
             <dependency>
-                <groupId>net.sf</groupId>
-                <artifactId>sam</artifactId>
-                <version>${sam.version}</version>
+                <groupId>samtools</groupId>
+                <artifactId>htsjdk</artifactId>
+                <version>${htsjdk.version}</version>
                 <exclusions>
                     <exclusion>
                         <groupId>org.testng</groupId>
@@ -80,20 +77,10 @@
                 </exclusions>
             </dependency>
             <dependency>
-                <groupId>net.sf</groupId>
+                <groupId>picard</groupId>
                 <artifactId>picard</artifactId>
                 <version>${picard.version}</version>
             </dependency>
-            <dependency>
-                <groupId>org.broad</groupId>
-                <artifactId>tribble</artifactId>
-                <version>${tribble.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.broadinstitute</groupId>
-                <artifactId>variant</artifactId>
-                <version>${variant.version}</version>
-            </dependency>
             <dependency>
                 <groupId>log4j</groupId>
                 <artifactId>log4j</artifactId>
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index fddd43946..ab4b7e1b7 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -21,21 +21,13 @@
 
     <dependencies>
         <dependency>
-            <groupId>net.sf</groupId>
-            <artifactId>sam</artifactId>
+            <groupId>samtools</groupId>
+            <artifactId>htsjdk</artifactId>
         </dependency>
         <dependency>
-            <groupId>net.sf</groupId>
+            <groupId>picard</groupId>
             <artifactId>picard</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.broad</groupId>
-            <artifactId>tribble</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.broadinstitute</groupId>
-            <artifactId>variant</artifactId>
-        </dependency>
         <dependency>
             <groupId>log4j</groupId>
             <artifactId>log4j</artifactId>