diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/DownsampleReadsQC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/DownsampleReadsQC.java
deleted file mode 100644
index 1141a9164..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/DownsampleReadsQC.java
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * Copyright (c) 2012 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.gatk.walkers.readutils;
-
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.downsampling.DownsamplingUtils;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.LinkedList;
-
-/**
- */
-@Requires({DataSource.READS, DataSource.REFERENCE})
-public class DownsampleReadsQC extends ReadWalker<GATKSAMRecord, Collection<GATKSAMRecord>> implements NanoSchedulable {
-    @Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
-    StingSAMFileWriter out;
-
-    @Argument(fullName = "minReadsPerAlignmentStart", shortName = "minReadsPerAlignmentStart", doc ="", required = false)
-    private int minReadsPerAlignmentStart = 5;
-
-    @Argument(fullName = "downsampleTo", shortName = "downsampleTo", doc ="", required = false)
-    private int downsampleTo = 1000;
-
-    /**
-     * The initialize function.
-     */
-    public void initialize() {
-//        final boolean preSorted = true;
-//        if (getToolkit() != null && getToolkit().getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) {
-//            Utils.setupWriter(out, getToolkit(), getToolkit().getSAMFileHeader(), !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
-//        }
-    }
-
-    /**
-     * The reads map function.
-     *
-     * @param ref  the reference bases that correspond to our read, if a reference was provided
-     * @param readIn the read itself, as a GATKSAMRecord
-     * @return the read itself
-     */
-    public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord readIn, RefMetaDataTracker metaDataTracker ) {
-        return readIn;
-    }
-
-    /**
-     * reduceInit is called once before any calls to the map function.  We use it here to setup the output
-     * bam file, if it was specified on the command line
-     *
-     * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
-     */
-    public Collection<GATKSAMRecord> reduceInit() {
-        return new LinkedList<GATKSAMRecord>();
-    }
-
-    /**
-     * given a read and a output location, reduce by emitting the read
-     *
-     * @param read   the read itself
-     * @param output the output source
-     * @return the SAMFileWriter, so that the next reduce can emit to the same source
-     */
-    public Collection<GATKSAMRecord> reduce( GATKSAMRecord read, Collection<GATKSAMRecord> output ) {
-        output.add(read);
-        return output;
-    }
-
-    @Override
-    public void onTraversalDone(Collection<GATKSAMRecord> result) {
-        for ( final GATKSAMRecord read : DownsamplingUtils.levelCoverageByPosition(new ArrayList<GATKSAMRecord>(result), downsampleTo, minReadsPerAlignmentStart) )
-            out.addAlignment(read);
-    }
-}