diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
deleted file mode 100644
index 306509d0c..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
+++ /dev/null
@@ -1,118 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.phasing;
-
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-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.RodWalker;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-
-import java.util.*;
-
-/**
- * Merges read-back-phased and phase-by-transmission files.
- */
-public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
-    @Output
-    protected VCFWriter vcfWriter = null;
-
-    @Input(fullName="pbt", shortName = "pbt", doc="Input VCF truth file", required=true)
-    public RodBinding<VariantContext> pbtTrack;
-
-    @Input(fullName="rbp", shortName = "rbp", doc="Input VCF truth file", required=true)
-    public RodBinding<VariantContext> rbpTrack;
-
-    private Map<String, Genotype> pbtCache = new HashMap<String, Genotype>();
-    private Map<String, Genotype> rbpCache = new HashMap<String, Genotype>();
-
-    private final String SOURCE_NAME = "MergeReadBackedAndTransmissionPhasedVariants";
-
-    public void initialize() {
-        ArrayList<String> rodNames = new ArrayList<String>();
-        rodNames.add(pbtTrack.getName());
-
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
-        Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
-        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
-        headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
-
-        vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples));
-    }
-
-    @Override
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if (tracker != null) {
-            Collection<VariantContext> pbts = tracker.getValues(pbtTrack, ref.getLocus());
-            Collection<VariantContext> rbps = tracker.getValues(rbpTrack, ref.getLocus());
-
-            VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
-            VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;
-
-            if (pbt != null && rbp != null) {
-                Map<String, Genotype> genotypes = pbt.getGenotypes();
-
-                if (!rbp.isFiltered()) {
-                    for (String sample : rbp.getSampleNames()) {
-                        Genotype rbpg = rbp.getGenotype(sample);
-                        Genotype pbtg = pbt.getGenotype(sample);
-
-                        // Propagate read-backed phasing information to genotypes unphased by transmission
-                        //if (!pbtg.isPhased() && rbpCache.containsKey(sample)) {
-                        if (!pbtg.isPhased() && rbpg.isPhased() && rbpCache.containsKey(sample)) {
-                            boolean orientationMatches = rbpCache.get(sample).sameGenotype(pbtCache.get(sample), false);
-
-                            if (orientationMatches) {
-                                pbtg = rbpg;
-                            } else {
-                                List<Allele> fwdAlleles = rbpg.getAlleles();
-                                List<Allele> revAlleles = new ArrayList<Allele>();
-
-                                for (int i = fwdAlleles.size() - 1; i >= 0; i--) {
-                                    revAlleles.add(fwdAlleles.get(i));
-                                }
-
-                                pbtg = new Genotype(sample, revAlleles, rbpg.getNegLog10PError(), rbpg.getFilters(), rbpg.getAttributes(), rbpg.isPhased());
-                            }
-                        }
-
-                        genotypes.put(sample, pbtg);
-
-                        // Update the cache
-                        if (/*rbpg.isPhased() &&*/ rbpg.isHet()) {
-                            rbpCache.put(sample, rbpg);
-                            pbtCache.put(sample, pbtg);
-                        } else if (!rbpg.isPhased()) {
-                            rbpCache.remove(sample);
-                            pbtCache.remove(sample);
-                        }
-                    }
-                }
-
-                VariantContext newvc = new VariantContext(SOURCE_NAME, pbt.getChr(), pbt.getStart(), pbt.getStart(), pbt.getAlleles(), genotypes, pbt.getNegLog10PError(), pbt.getFilters(), pbt.getAttributes());
-                vcfWriter.add(newvc);
-            }
-        }
-
-        return null;
-    }
-
-    @Override
-    public Integer reduceInit() {
-        return null;
-    }
-
-    @Override
-    public Integer reduce(Integer value, Integer sum) {
-        return null;
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
deleted file mode 100644
index cf6b4e581..000000000
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.phasing;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-
-public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest {
-    private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeAndMatchHaplotypes";
-    private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf";
-    private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf";
-
-    @Test
-    public void testBasicFunctionality() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                buildCommandLine(
-                        "-T MergeAndMatchHaplotypes",
-                        "-R " + b37KGReference,
-                        "--pbt " + fundamentalTestPBTVCF,
-                        "--rbp " + fundamentalTestRBPVCF,
-                        "-o %s"
-                ),
-                1,
-                Arrays.asList("")
-        );
-        executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec);
-    }
-}