diff --git a/build.xml b/build.xml
index 881e741ed..a85e16e4a 100644
--- a/build.xml
+++ b/build.xml
@@ -358,6 +358,24 @@
           </manifest>
         </jar>
 
+        <jar jarfile="${dist.dir}/ReorderSam.jar" whenmanifestonly="skip">
+          <fileset dir="${java.classes}">
+            <include name="**/tools/**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.ReorderSam" />
+          </manifest>
+        </jar>
+
+        <jar jarfile="${dist.dir}/CompareBAMAlignments.jar" whenmanifestonly="skip">
+          <fileset dir="${java.classes}">
+            <include name="**/tools/**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.CompareBAMAlignments" />
+          </manifest>
+        </jar>
+
         <subant target="dist" genericantfile="build.xml">
             <property name="build.dir" value="${external.build.dir}" />
             <property name="dist.dir" value="${external.dist.dir}" />
@@ -420,6 +438,18 @@
             </manifest>
         </jar>
 
+        <jar jarfile="${dist.dir}/CompareBAMAlignments.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
+
+        <jar jarfile="${dist.dir}/ReorderSam.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
+
     </target>
 
     <target name="queue.manifests" depends="queue.jar, init.manifests" if="scala.include">