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
new file mode 100644
index 000000000..4da049b39
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
@@ -0,0 +1,107 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+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.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.*;
+
+public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
+    @Output
+    protected VCFWriter vcfWriter = null;
+
+    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("pbt");
+
+        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.getVariantContexts(ref, "pbt", null, ref.getLocus(), true, true);
+            Collection<VariantContext> rbps = tracker.getVariantContexts(ref, "rbp", null, ref.getLocus(), true, true);
+
+            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, ref.getBase());
+            }
+        }
+
+        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
new file mode 100644
index 000000000..46d96da27
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
@@ -0,0 +1,28 @@
+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 + "/MergeByHaplotypes";
+    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,
+                        "-B:pbt,VCF " + fundamentalTestPBTVCF,
+                        "-B:rbp,VCF " + fundamentalTestRBPVCF,
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("")
+        );
+        executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec);
+    }
+}