diff --git a/build.xml b/build.xml
index b27893493..b93b0d200 100644
--- a/build.xml
+++ b/build.xml
@@ -419,6 +419,15 @@
             <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.CompareBAMAlignments" />
           </manifest>
         </jar>
+
+        <jar jarfile="${dist.dir}/SliceBams.jar" whenmanifestonly="skip">
+          <fileset dir="${java.classes}">
+            <include name="**/tools/**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.SliceBams" />
+          </manifest>
+        </jar>
     </target>
 
     <target name="scala.jar" depends="scala.compile, init.jar" if="scala.include">
@@ -483,6 +492,11 @@
                 <attribute name="Class-Path" value="${jar.classpath}" />
             </manifest>
         </jar>
+        <jar jarfile="${dist.dir}/SliceBams.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">
diff --git a/java/src/org/broadinstitute/sting/playground/tools/SliceBams.java b/java/src/org/broadinstitute/sting/playground/tools/SliceBams.java
new file mode 100644
index 000000000..29354013c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/tools/SliceBams.java
@@ -0,0 +1,162 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package org.broadinstitute.sting.playground.tools;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Option;
+import net.sf.picard.cmdline.StandardOptionDefinitions;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.io.IoUtil;
+import net.sf.picard.sam.MergingSamRecordIterator;
+import net.sf.picard.sam.SamFileHeaderMerger;
+import net.sf.picard.util.Log;
+import net.sf.samtools.*;
+import net.sf.samtools.util.BlockCompressedOutputStream;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter;
+import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.ArrayBlockingQueue;
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * Reads a list of BAM files and slices all of them into a single merged BAM file
+ * containing reads in overlapping chr:start-stop interval.
+ *
+ * @author Mark DePristo
+ */
+public class SliceBams extends CommandLineProgram {
+    private static final Log log = Log.getInstance(SliceBams.class);
+
+    // Usage and parameters
+    @Usage
+    public String USAGE = "Merges multiple SAM/BAM files into one BAM overlapping chr:start-stop interval .\n";
+
+    @Option(shortName="I", doc="List of input BAM files")
+    public File INPUT_LIST;
+
+    @Option(shortName="O", doc="SAM or BAM file to write merged result to")
+    public File OUTPUT;
+
+    @Option(shortName="L", doc="Location to include")
+    public String SLICE;
+
+    private static final int PROGRESS_INTERVAL = 1000000;
+
+    /** Required main method implementation. */
+    public static void main(final String[] argv) {
+        System.exit(new SliceBams().instanceMain(argv));
+    }
+
+    private List<File> parseInputFiles(File list) {
+        try {
+            final List<File> files = new ArrayList<File>();
+            for (String fileName : new XReadLines(list).readLines() ) {
+                files.add(new File(fileName));
+            }
+            return files;
+        } catch ( FileNotFoundException e ) {
+            throw new PicardException("Couldn't read input list", e);
+        }
+    }
+
+    /**
+     * Walk over the input files, reading the headers, and finally prepare the output
+     * BAM containing a merge of all of the headers.
+     *
+     * @param inputBAMs
+     * @return
+     */
+    private SAMFileWriter createOutputBAM(List<File> inputBAMs) {
+        SAMFileHeader header = null;
+
+        log.info("Reading headers");
+        int fileCounter = 1;
+        for (final File inFile : inputBAMs) {
+            IoUtil.assertFileIsReadable(inFile);
+            final SAMFileReader inReader = new SAMFileReader(inFile, null); // null because we don't want it to look for the index
+            final SAMFileHeader inHeader = inReader.getFileHeader();
+            log.info("  Reading header from file " + inFile + " " + fileCounter++ + " of " + inputBAMs.size());
+
+            if (header == null) {
+                header = inHeader;
+            }
+            else {
+                for ( SAMReadGroupRecord rg : inHeader.getReadGroups() )
+                    header.addReadGroup(rg);
+            }
+
+            inReader.close();
+        }
+
+        SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUTPUT);
+        return new SimplifyingSAMFileWriter(out);
+    }
+
+    /** Combines multiple SAM/BAM files into one. */
+    @Override
+	protected int doWork() {
+        SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+        SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true);
+
+        // Open the files for reading and writing
+        List<File> inputBAMs = parseInputFiles(INPUT_LIST);
+        IoUtil.assertFileIsWritable(OUTPUT);
+        final SAMFileWriter out = createOutputBAM(inputBAMs);
+        GenomeLocParser glParser = new GenomeLocParser(out.getFileHeader().getSequenceDictionary());
+        GenomeLoc loc = glParser.parseGenomeLoc(SLICE);
+
+        log.info("Reading BAM records");
+        long numRecords = 1;
+        int fileCounter = 1;
+        for (final File inFile : inputBAMs) {
+            IoUtil.assertFileIsReadable(inFile);
+            log.info("  Reading file " + inFile + " " + fileCounter++ + " of " + inputBAMs.size());
+            final SAMFileReader reader = new SAMFileReader(inFile);
+            SAMRecordIterator iterator = reader.queryOverlapping(loc.getContig(), loc.getStart(), loc.getStop());
+
+            while ( iterator.hasNext() ) {
+                final SAMRecord record = iterator.next();
+                out.addAlignment(record);
+                if (numRecords % PROGRESS_INTERVAL == 0) {
+                    log.info(numRecords + " records read.");
+                }
+            }
+
+            reader.close();
+        }
+
+        log.info("Finished reading inputs.");
+        log.info("Sorting final output file.");
+        out.close();
+        return 0;
+    }
+}