diff --git a/build.xml b/build.xml
index 038c4f916..d640e6339 100644
--- a/build.xml
+++ b/build.xml
@@ -293,23 +293,6 @@
           </manifest>
         </jar>
 
-        <jar jarfile="${dist.dir}/CGUtilities.jar" whenmanifestonly="skip">
-          <fileset dir="${java.classes}">
-            <include name="**/*.class" />
-          </fileset>
-          <manifest>
-            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.CGUtilities" />
-          </manifest>
-        </jar>
-
-	   <jar jarfile="${dist.dir}/VCFTool.jar" whenmanifestonly="skip">
-          <fileset dir="${java.classes}">
-            <include name="**/*.class"/>
-          </fileset>
-          <manifest>
-            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.vcf.VCFTool" />
-          </manifest>
-        </jar>
     </target>
 
     <target name="queue.jar" depends="queue.compile, queue-gatk-extensions.compile, init.jar" if="queue.include">
@@ -349,12 +332,6 @@
 
     <target name="gatk.manifests" depends="gatk.jar, init.manifests">
 
-        <jar jarfile="${dist.dir}/VCFTool.jar" update="true" >
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
-
         <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar" update="true">
             <manifest>
                 <attribute name="Class-Path" value="${jar.classpath}"/>
@@ -367,12 +344,6 @@
             </manifest>
         </jar>
 
-        <jar jarfile="${dist.dir}/CGUtilities.jar" update="true" whenmanifestonly="skip">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
-
     </target>
 
     <target name="queue.manifests" depends="queue.jar, init.manifests" if="queue.include">
diff --git a/java/src/org/broadinstitute/sting/playground/tools/CGUtilities.java b/java/src/org/broadinstitute/sting/playground/tools/CGUtilities.java
deleted file mode 100755
index dd1d69690..000000000
--- a/java/src/org/broadinstitute/sting/playground/tools/CGUtilities.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package org.broadinstitute.sting.playground.tools;
-
-import net.sf.picard.cmdline.CommandLineProgram;
-import net.sf.picard.cmdline.Usage;
-import net.sf.picard.cmdline.Option;
-import net.sf.samtools.*;
-
-import java.io.*;
-import java.util.List;
-import java.util.ArrayList;
-
-public class CGUtilities extends CommandLineProgram {
-    @Usage(programVersion="1.0") public String USAGE = "Mark, document me";
-    @Option(shortName="I", doc="Input file (bam or sam) to mark primary alignments in.  Must be sorted by name",
-                optional=false) public File IN = null;
-    @Option(shortName="O",doc="Output file (BAM). If not specified, output is printed to stdout.",
-            optional=false) public File OUT = null;
-    @Option(shortName="M",doc="Maximum number of reasd to process.",
-            optional=true) public int MAX_READS = -1;
-
-    public static void main(final String[] argv) {
-        System.exit(new CGUtilities().instanceMain(argv));
-    }
-
-    protected int doWork() {
-        InputStream ins;
-        try {
-            ins = new FileInputStream(IN);
-        } catch ( FileNotFoundException ie ) {
-            System.out.println("Failed to open input file "+IN+": "+ie.getCause());
-            return 1;
-        }
-
-        SAMFileReader inReader = new SAMFileReader(ins);
-        SAMFileHeader header = inReader.getFileHeader();
-        header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
-        SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUT);
-
-        int i = 0;
-        String currentReadName = null;
-        List<SAMRecord> possibleAlignments = new ArrayList<SAMRecord>();
-
-        for ( SAMRecord read : inReader ) {
-            String readName = read.getReadName();
-            //System.out.println("@" + readName);
-
-            if ( currentReadName == null )
-                currentReadName = readName;
-
-            if ( ! currentReadName.equals(readName) ) {
-                List<SAMRecord> firsts = subsetByPair(possibleAlignments, true);
-                List<SAMRecord> seconds = subsetByPair(possibleAlignments, false);
-
-                if ( firsts.size() + seconds.size() != possibleAlignments.size() ) {
-                    throw new RuntimeException(String.format("Dropped reads %d + %d != %d at %s%n", firsts.size(), seconds.size(), possibleAlignments.size(), currentReadName));
-                }
-
-                if ( firsts.size() > 0 ) out.addAlignment(selectBestAlignment(firsts));
-                if ( seconds.size() > 0 ) out.addAlignment(selectBestAlignment(seconds));
-                possibleAlignments.clear();
-                currentReadName = readName;
-            }
-
-            possibleAlignments.add(read);
-
-            //out.addAlignment(read);
-            if ( i++ > MAX_READS && MAX_READS != -1 ) break;
-        }
-        inReader.close();
-        out.close();
-
-        return 0;
-    }
-
-    protected SAMRecord selectBestAlignment(List<SAMRecord> possibleAlignments) {
-        SAMRecord best = null;
-        for ( SAMRecord possible : possibleAlignments ) {
-            if ( best == null || isBetterAlignment(best, possible) )
-                best = possible;
-        }
-
-        if ( best != null ) {
-            best.setNotPrimaryAlignmentFlag(false); // we're the primary alignment!
-        }
-
-        return best;
-    }
-
-    protected List<SAMRecord> subsetByPair(List<SAMRecord> reads, boolean getFirst) {
-        List<SAMRecord> sub = new ArrayList<SAMRecord>();
-
-        for ( SAMRecord read : reads ) {
-            boolean add = read.getFirstOfPairFlag() ? getFirst : ! getFirst;
-            if ( ! read.getReadPairedFlag() )
-                throw new RuntimeException("Read is unpaired! " + read.format());
-            if ( add ) sub.add(read);
-        }
-        
-        return sub;
-    }
-
-    protected boolean isBetterAlignment(SAMRecord champ, SAMRecord contender) {
-        boolean replace = false;
-        if ( contender.getMappingQuality() >= champ.getMappingQuality() ) {
-            if ( contender.getMappingQuality() > champ.getMappingQuality() ) {
-                replace = true;
-            } else if ( contender.getReadLength() > champ.getReadLength() ) {
-                replace = true;
-            } else {
-                ;
-                //System.out.printf("Equivalent reads%n  %s%n  %s%n", champ.format(), contender.format());
-            }
-        }
-
-        //if ( replace )
-        //    System.out.printf("Better read %n  %s%n  %s%n", contender.format(), champ.format());
-
-        //System.out.printf("Comparing %s vs. %s => contender is better? %s%n", champ, contender, replace);
-
-        return replace;
-    }
-}
\ No newline at end of file