diff --git a/build.xml b/build.xml
index 4acb2086a..85955d774 100644
--- a/build.xml
+++ b/build.xml
@@ -43,6 +43,9 @@
     <property name="scala.classes" value="${build.dir}/scala/classes" />
 
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
+
+    <property name="javadoc.dir" value="javadoc" />
+    <property name="scaladoc.dir" value="scaladoc" />
     
     <!-- Contracts for Java -->
     <!-- To disable, run with -Duse.contracts=false -->
@@ -50,9 +53,6 @@
     <property name="java.contracts" value="${build.dir}/java/contracts" />
     <property name="contracts.version" value="1.0-20110609" />
     <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
-    
-    <!-- where to find the tribble distro -->
-    <property name="tribble.dir" value="tribble" />
 
     <!-- where to find 'findbugs', which you must set if you plan to use 'ant findbugs' -->
     <property name="findbugs.home" value="./findbugs"/>
@@ -89,7 +89,6 @@
         <patternset refid="all.java.source.pattern" />
     </fileset>
 
-
     <fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
         <include name="**/*.java" />
     </fileset>
@@ -171,6 +170,12 @@
         <property name="scala.target" value="core"/>
     </target>
 
+    <target name="init.buildpublic">
+        <!-- Set the properties needed to build public only -->
+        <property name="gatk.target" value="core"/>
+        <property name="scala.target" value="core"/>
+    </target>
+
     <target name="git.describe">
       <exec executable="git" outputproperty="git.describe.output" resultproperty="git.describe.exit.value" failonerror="false">
         <arg line="describe" />
@@ -245,6 +250,7 @@
 
       <!-- Create the build directory structure used by compile -->
       <mkdir dir="${build.dir}"/>
+      <mkdir dir="${lib.dir}"/>
       <mkdir dir="${java.classes}"/>
       <mkdir dir="${java.contracts}"/>
 
@@ -276,7 +282,7 @@
         </taskdef>
     </target>
 
-    <target name="gatk.compile.public.source" depends="tribble,init,resolve">
+    <target name="gatk.compile.public.source" depends="init,resolve">
         <javac fork="true" srcdir="${java.public.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
           <compilerarg value="-proc:none"/>
         </javac>    
@@ -337,7 +343,7 @@
     <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" 
             description="create GATK contracts" if="include.contracts" />
     
-    <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
+    <target name="gatk.compile" depends="init,resolve,gatk.compile.source,gatk.contracts" />
 
     <target name="init.queue-extensions.generate" depends="gatk.compile">
         <condition property="uptodate.queue-extensions.generate">
@@ -863,7 +869,7 @@
     </macrodef>
 
     <!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
-    <target name="test" depends="test.compile,tribble.test" description="Run unit tests">
+    <target name="test" depends="test.compile" description="Run unit tests">
         <condition property="ttype" value="*UnitTest" else="${single}">
             <not><isset property="single"/></not>
         </condition>
@@ -911,86 +917,59 @@
         <run-failed-test xmlfailedtestfile="${report}/*PipelineTest/testng-failed.xml" />
     </target>
 
-    <!-- ***************************************************************************** -->
-    <!-- ***********                     Tribble                             ********* -->
-    <!-- ***************************************************************************** -->
-    <target name="tribble.init" description="checks if tribble is available to build from source">
-        <condition property="tribble.compile.exists">
-            <available file="${tribble.dir}/build.xml"/>
-        </condition>
-    </target>
-
-    <!-- compile the library -->
-    <target name="tribble.compile" description="compiles the tribble library" depends="tribble.init" if="tribble.compile.exists">
-        <echo message="Building the Tribble Library..."/>
-        <ant antfile="build.xml" target="all" dir="${tribble.dir}" inheritAll="false"/>
-    </target>
-
-    <!-- copy the compiled library -->
-    <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
-        <copy todir="${lib.dir}">
-            <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
-        </copy>
-    </target>
-
-    <!-- copy the precompiled library -->
-    <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
-        <echo message="Copying the Tribble Library..."/>
-        <copy todir="${lib.dir}">
-            <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
-        </copy>
-    </target>
-
-    <target name="tribble" description="Copies the tribble jar" depends="tribble.compile.copy,tribble.library.copy"/>
-
-    <target name="tribble.test.init" description="runs the tribble tests" depends="tribble.init">
-        <condition property="tribble.test.run">
-            <and>
-                <isset property="tribble.compile.exists"/>
-                <not><isset property="single"/></not>
-            </and>
-        </condition>
-    </target>
-
-    <!-- test tribble using the unit tests set in tribble -->
-    <target name="tribble.test" description="runs the tribble tests" depends="tribble.test.init,tribble.compile" if="tribble.test.run">
-        <echo message="Testing the Tribble Library..."/>
-        <ant antfile="build.xml" target="test" dir="${tribble.dir}" inheritAll="false"/>
-    </target>
-
-    <!-- clean tribble -->
-    <target name="tribble.clean" description="cleans the tribble library" depends="tribble.init" if="tribble.compile.exists">
-        <echo message="Cleaning the Tribble Library..."/>
-        <ant antfile="build.xml" target="clean" dir="${tribble.dir}" inheritAll="false"/>
-    </target>
-    <!-- ***************************************************************************** -->
+    <!-- ******************************************************************************** -->
+    <!-- Javadoc                                                                          -->
+    <!-- ******************************************************************************** -->
 
     <target name="clean.javadoc">
-        <delete dir="javadoc"/>
-        <delete dir="scaladoc"/>
+        <delete dir="${javadoc.dir}" />
     </target>
 
-    <target name="javadoc" depends="init.buildall,resolve,queue-extensions.generate,init.scala.compile" description="generates javadoc">
-        <mkdir dir="javadoc"/>
-        <javadoc destdir="javadoc"
-                 classpathref="external.dependencies">
-            <sourcepath path="${java.public.source.dir}"/>
-            <sourcepath path="${external.dir}"/>
+    <target name="init.javadoc">
+        <mkdir dir="${javadoc.dir}" />
+    </target>
+
+    <target name="javadoc" depends="init.buildpublic,generate.javadoc" description="Generates public javadoc" />
+
+    <target name="javadoc.private" depends="init.buildall,generate.javadoc" description="Generates public and private javadoc" />
+
+    <target name="generate.javadoc" depends="init.javadoc,resolve">
+        <javadoc destdir="${javadoc.dir}" classpathref="external.dependencies">
+            <fileset refid="java.source.files" />
+            <sourcepath path="${external.dir}" />
         </javadoc>
-        <javadoc destdir="javadoc"
-                 classpathref="external.dependencies">
-            <sourcepath path="${java.private.source.dir}"/>
-            <exclude name="**" unless="include.private" />
-        </javadoc>        
-        <mkdir dir="scaladoc"/>
-        <scaladoc srcdir="" destdir="scaladoc" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
-            <src path="${scala.public.source.dir}"/>
-            <src path="${scala.private.source.dir}"/>
-            <src path="${queue-extensions.source.dir}"/>
-            <include name="**/*.scala"/>
+    </target>
+
+    <!-- ******************************************************************************** -->
+    <!-- Scaladoc                                                                         -->
+    <!-- ******************************************************************************** -->
+
+    <target name="clean.scaladoc">
+        <delete dir="${scaladoc.dir}" />
+    </target>
+
+    <target name="init.scaladoc">
+        <mkdir dir="${scaladoc.dir}" />
+    </target>
+
+    <!-- NOTE: the scaladoc targets require that the environment variable ANT_OPTS has been set to "-Xmx1G" -->
+
+    <target name="scaladoc" depends="init.buildpublic,generate.scaladoc" description="Generates public scaladoc -- set ANT_OPTS to -Xmx1G" />
+
+    <target name="scaladoc.private" depends="init.buildall,generate.scaladoc" description="Generates public and private scaladoc -- set ANT_OPTS to -Xmx1G" />
+
+    <target name="generate.scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc">
+        <scaladoc srcdir="${basedir}" destdir="${scaladoc.dir}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
+            <include name="${scala.public.source.dir}/**/*.scala" />
+            <include name="${queue-extensions.source.dir}/**/*.scala" />
+            <include name="${scala.private.source.dir}/**/*.scala" if="include.private" />
         </scaladoc>
     </target>
 
+    <!-- ******************************************************************************** -->
+    <!-- Release-related tasks                                                            -->
+    <!-- ******************************************************************************** -->
+
     <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
     <target name="stage" description="stage files for distribution">
         <mkdir dir="staging"/>
@@ -1080,7 +1059,7 @@
        </findbugs>
     </target>
 
-    <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc,clean.gatkdocs">
+    <target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs">
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
         <delete dir="${lib.dir}"/>
diff --git a/ivy.xml b/ivy.xml
index a394aa6d7..115f4062a 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -12,6 +12,9 @@
     <dependency org="net.sf" name="picard" rev="latest.integration"/>
     <dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>
 
+    <!-- Tribble -->
+    <dependency org="org.broad" name="tribble" rev="latest.integration"/>
+
     <dependency org="log4j" name="log4j" rev="1.2.15">
       <!-- Don't include javax.mail here in default, only used in scala->default by commons-email -->
       <exclude org="javax.mail" />
diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 7a749c0a2..63faf1ab9 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -67,6 +67,7 @@ public abstract class BaseTest {
     public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
     public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
     public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
+    public static final String hg18dbSNP132 = dbsnpDataLocation + "dbsnp_132.hg18.vcf";
 
     public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
     public static final String b37hapmapGenotypes = hapmapDataLocation + "genotypes_r27_nr.b37_fwd.vcf";
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index d11fb7e29..da0c8f81f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -16,8 +16,8 @@ import java.util.Map;
 
 public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
-    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH";
-    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL";
+    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129;
+    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129;
 
     // --------------------------------------------------------------------------------------------------------------
     //
@@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("16b0c7b47745abcd1ddaa2e261719530"));
+                Arrays.asList("149e6ad9b3fd23551254a691286a96b3"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("811ddc0bd8322b14f14f58df8c627aa9"));
+                Arrays.asList("8de2602679ffc92388da0b6cb4325ef6"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("5cf08dd7ac3d218082f7be3915ce0b15"));
+                Arrays.asList("ec43daadfb15b00b41aeb0017a45df0b"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -67,7 +67,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("75156264696563c2f47620fef9424f7c"));
+                Arrays.asList("82d469145c174486ccc494884852cc58"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
@@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "7255e03430549cb97d8fcae34cbffb02";
+    private final static String COMPRESSED_OUTPUT_MD5 = "a5a9f38c645d6004d4640765a8b77ce4";
 
     @Test
     public void testCompressedOutput() {
@@ -107,7 +107,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
 
-        String md5 = "7912109e83fda21dae90ef8d5dd0140d";
+        String md5 = "0a45761c0e557d9c2080eb9e7f4f6c41";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -138,10 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testCallingParameters() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "--min_base_quality_score 26", "6d3aa9f783ca63f37c952f83eeda593c" );
-        e.put( "--min_mapping_quality_score 26", "51bfdf777123bf49de5d92ffde5c74e7" );
-        e.put( "--p_nonref_model GRID_SEARCH", "333328ab2c8da2875fade599e80a271f" );
-        e.put( "--computeSLOD", "226caa28a4fa9fe34f3beb8a23f3d53d" );
+        e.put( "--min_base_quality_score 26", "531966aee1cd5dced61c96c4fedb59a9" );
+        e.put( "--min_mapping_quality_score 26", "c71ca370947739cb7d87b59452be7a07" );
+        e.put( "--computeSLOD", "1a5648f26c18ced27df4be031b44e72d" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -154,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testOutputParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-sites_only", "5f659dee408710d3709ed72005cd863a" );
-        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "55d09bf13149bddc06cc36be0801507b" );
-        e.put( "--output_mode EMIT_ALL_SITES", "727f49dcb2439b18446829efc3b1561c" );
+        e.put( "-sites_only", "d40114aa201aa33ff5f174f15b6b73af" );
+        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3c681b053fd2280f3c42041d24243752" );
+        e.put( "--output_mode EMIT_ALL_SITES", "eafa6d71c5ecd64dfee5d7a3f60e392e" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -170,12 +169,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("51bfdf777123bf49de5d92ffde5c74e7"));
+                Arrays.asList("c71ca370947739cb7d87b59452be7a07"));
         executeTest("test confidence 1", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
-                Arrays.asList("c67c285e70fd4457c9f9ce7bd878ddca"));
+                Arrays.asList("1c0a599d475cc7d5e745df6e9b6c0d29"));
         executeTest("test confidence 2", spec2);
     }
 
@@ -187,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testHeterozyosity() {
         HashMap<Double, String> e = new HashMap<Double, String>();
-        e.put( 0.01, "7ecc564d4db97d5932cef2e558550ed2" );
-        e.put( 1.0 / 1850, "aa9e101bb9f9e111fe292fec467d915a" );
+        e.put( 0.01, "af5199fbc0853cf5888acdcc88f012bc" );
+        e.put( 1.0 / 1850, "4e6938645ccde1fdf204ffbf4e88170f" );
 
         for ( Map.Entry<Double, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -212,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("2efd686186b2c5129be4cf89274a24dd"));
+                Arrays.asList("213ebaaaacf850312d885e918eb33500"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -231,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("2892d35331fe9fc141ba19269ec7caed"));
+                Arrays.asList("3aecba34a89f3525afa57a38dc20e6cd"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -250,7 +249,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("8c2afb4289ed44521933d1a74c8d6c7f"));
+                Arrays.asList("043973c719a85de29a35a33a674616fb"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -265,7 +264,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("b6fb70590a10e1c27fb611732916f27d"));
+                Arrays.asList("68d4e6c1849e892467aed61c33e7bf24"));
 
         executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
     }
@@ -278,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("61642502bd08cc03cdaaeb83a5426b46"));
+                 Arrays.asList("f86d453c5d2d2f33fb28ae2050658a5e"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -288,14 +287,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("69b0b3f089c80b9864294d838a061336"));
+                Arrays.asList("408d3aba4d094c067fc00a43992c2292"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("c90174cfd7dd68bdef36fe2c60145e10"));
+                Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
index fb7e84d22..3ff453dab 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
@@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
-                        " --dbsnp:VCF " + b36dbSNP129 +
+                        " --dbsnp:VCF " + hg18dbSNP132 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
@@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
-                        " --dbsnp:vcf " + b36dbSNP129 +
+                        " --dbsnp:vcf " + hg18dbSNP132 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
@@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -L chr1:1-50,000,000" +
                         " -nt 10" +
-                        " --dbsnp:vcf " + b36dbSNP129 +
+                        " --dbsnp:vcf " + hg18dbSNP132 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
index 43ea401f7..bccb95795 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
@@ -16,7 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L chr1:1-50,000,000" +
                         " -standard" +
                         " -OQ" +
-                        " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -recalFile /dev/null" + moreArgs,
                 0,
                 new ArrayList<String>(0));
@@ -31,7 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
                         " -standard" +
                         " -OQ" +
-                        " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -recalFile /dev/null" + moreArgs,
                 0,
                 new ArrayList<String>(0));
diff --git a/settings/repository/org.broad/tribble-16.xml b/settings/repository/org.broad/tribble-16.xml
deleted file mode 100644
index e23eec339..000000000
--- a/settings/repository/org.broad/tribble-16.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="15" 
-          status="integration" publication="" />
-</ivy-module>
diff --git a/settings/repository/org.broad/tribble-16.jar b/settings/repository/org.broad/tribble-18.jar
similarity index 87%
rename from settings/repository/org.broad/tribble-16.jar
rename to settings/repository/org.broad/tribble-18.jar
index 331f28ec3..1ea101dd0 100644
Binary files a/settings/repository/org.broad/tribble-16.jar and b/settings/repository/org.broad/tribble-18.jar differ
diff --git a/settings/repository/org.broad/tribble-18.xml b/settings/repository/org.broad/tribble-18.xml
new file mode 100644
index 000000000..d2648ddad
--- /dev/null
+++ b/settings/repository/org.broad/tribble-18.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="org.broad" module="tribble" revision="18" status="integration" />
+</ivy-module>