diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
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+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
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+/*
+ * Copyright (c) 2010, 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.variantutils;
+
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.StandardVCFWriter;
+import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
+import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RMD;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.vcf.VCFUtils;
+
+import java.io.File;
+import java.util.*;
+
+/**
+ * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
+ */
+@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
+public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
+
+    @Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true)
+    protected VCFWriter vcfWriter1 = null;
+
+    @Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=true)
+    // there's a reported bug in the GATK where we can't have 2 @Output writers
+    protected File file2 = null;
+    protected StandardVCFWriter vcfWriter2 = null;
+
+    @Argument(fullName="fractionToOut1", shortName="fraction", doc="Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2", required=false)
+    protected double fraction = 0.5;
+
+    @Argument(fullName="randomSeed", shortName="seed", doc="Random seed to use; if 0, current time will be used", required=false)
+    protected long SEED = 0;
+
+    protected static final String INPUT_VARIANT_ROD_BINDING_NAME = "variant";
+
+    protected Random generator;
+    protected int iFraction;
+
+    /**
+     * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
+     */
+    public void initialize() {
+        if ( fraction < 0.0 || fraction > 1.0 )
+            throw new UserException.BadArgumentValue("fractionToOut1", "this value needs to be a number between 0 and 1");
+        iFraction = (int)(fraction * 1000.0);
+
+        // setup the header info
+        final ArrayList<String> inputNames = new ArrayList<String>();
+        inputNames.add( INPUT_VARIANT_ROD_BINDING_NAME );
+        Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
+        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+
+        vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
+        vcfWriter2 = new StandardVCFWriter(file2, true);
+        vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
+
+        if ( SEED == 0 )
+            generator = new Random();
+        else
+            generator = new Random(SEED);
+    }
+
+    /**
+     * Subset VC record if necessary and emit the modified record (provided it satisfies criteria for printing)
+     *
+     * @param  tracker   the ROD tracker
+     * @param  ref       reference information
+     * @param  context   alignment info
+     * @return 1 if the record was printed to the output file, 0 if otherwise
+     */
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null )
+            return 0;
+
+        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, null, context.getLocation(), true, false);
+        for ( VariantContext vc : vcs ) {
+            int random = generator.nextInt(1000);
+            if ( random < iFraction )
+                vcfWriter1.add(vc, ref.getBase());
+            else
+                vcfWriter2.add(vc, ref.getBase());
+        }
+
+        return 1;
+    }
+
+    public Integer reduceInit() { return 0; }
+
+    public Integer reduce(Integer value, Integer sum) { return value + sum; }
+
+    public void onTraversalDone(Integer result) { logger.info(result + " records processed."); }
+}