diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java
index e8e4a0a79..961014981 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java
@@ -5,10 +5,19 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariationRod;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.genotyper.SingleSampleGenotyper;
+import org.broadinstitute.sting.gatk.walkers.genotyper.SSGenotypeCall;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
 
+import java.util.Set;
+import java.util.List;
+import java.util.ArrayList;
+
+import net.sf.samtools.SAMRecord;
+
 /**
  * Created by IntelliJ IDEA.
  * User: andrewk
@@ -17,45 +26,82 @@ import org.broadinstitute.sting.utils.genotype.Variation;
  * To change this template use File | Settings | File Templates.
  */
 @By(DataSource.REFERENCE)
-@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="child",type= VariationRod.class), @RMD(name="parent1",type= VariationRod.class), @RMD(name="parent2",type= VariationRod.class)})
-//@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=AllelicVariant.class), @RMD(name="dbsnp",type=AllelicVariant.class),@RMD(name="hapmap-chip",type=AllelicVariant.class), @RMD(name="interval",type=IntervalRod.class)})
-//@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="dbsnp",type=AllelicVariant.class)})
+@Requires(value={DataSource.REFERENCE, DataSource.REFERENCE_BASES, DataSource.READS},referenceMetaData={@RMD(name="child",type= VariationRod.class)})
+@Allows({DataSource.READS, DataSource.REFERENCE})
+@ReadFilters(ZeroMappingQualityReadFilter.class)
+//, @RMD(name="parent1",type= VariationRod.class), @RMD(name="parent2",type= VariationRod.class)})
+
 public class DeNovoSNPWalker extends RefWalker<String, Integer>{
 
+    SingleSampleGenotyper SSG;
+    private List<Set<String>> readGroupSets;
+
+    public void initialize() {
+         SSG = new SingleSampleGenotyper();
+         SSG.initialize();
+
+         readGroupSets = getToolkit().getMergedReadGroupsByReaders();
+     }
+
     public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         Variation child = (Variation)tracker.lookup("child", null);
-        Variation parent1 = (Variation)tracker.lookup("parent1", null);
-        Variation parent2 = (Variation)tracker.lookup("parent2", null);
         Variation dbsnp = (Variation)tracker.lookup("dbSNP", null);
-        if (child != null && parent1 != null && parent2 != null) {
-            if (!(parent1 instanceof VariantBackedByGenotype) || !(parent2 instanceof VariantBackedByGenotype))
-                        throw new StingException("Both parents ROD tracks must be backed by genotype data. Ensure that your parent rod(s) contain genotyping information");
-            if (child.isSNP() &&
-                child.getNegLog10PError() > 5 && // BTR > 5
-                parent1.isReference() &&
-                ((VariantBackedByGenotype)parent1).getCalledGenotype().getNegLog10PError() > 5 &&
-                parent2.isReference() && 
-                ((VariantBackedByGenotype)parent2).getCalledGenotype().getNegLog10PError() > 5
+        if (child != null) {
+            if (child.isSNP() && child.getNegLog10PError() > 5) { // BTR > 5
+
+                List<SAMRecord> reads = context.getReads();
+                List<Integer> offsets = context.getOffsets();
+
+                List<SAMRecord> parent1_reads = new ArrayList<SAMRecord>();
+                List<SAMRecord> parent2_reads = new ArrayList<SAMRecord>();
+                List<Integer> parent1_offsets = new ArrayList<Integer>();
+                List<Integer> parent2_offsets = new ArrayList<Integer>();
+
+                assert( reads.size() == offsets.size() ); // should be same number or we're in trouble
+                int num_reads = reads.size();
+                for (int i=0; i<num_reads; i++) {
+                    SAMRecord read = reads.get(i);
+                    Integer offset = offsets.get(i);
+                    String readGroup = (String)read.getAttribute("RG");
+                    if (readGroupSets.get(0).contains(readGroup)) {
+                        parent1_reads.add(read);
+                        parent1_offsets.add(offset);
+                    } else if (readGroupSets.get(1).contains(readGroup)) {
+                        parent2_reads.add(read);
+                        parent2_offsets.add(offset);
+                    }
+                }
+
+                AlignmentContext parent1_subContext = new AlignmentContext(context.getLocation(), parent1_reads, parent1_offsets);
+                SSGenotypeCall parent1 = SSG.map(tracker, ref, parent1_subContext);
+
+                AlignmentContext parent2_subContext = new AlignmentContext(context.getLocation(), parent2_reads, parent2_offsets);
+                SSGenotypeCall parent2 = SSG.map(tracker, ref, parent2_subContext);
+
+                if (!parent1.isVariant(parent1.getReference()) &&
+                    parent1.getNegLog10PError() > 5 &&
+                    !parent2.isVariant(parent2.getReference()) &&
+                    parent2.getNegLog10PError() > 5
                 ) {
 
-                double sumConfidences = 0.5 * (0.5 * child.getNegLog10PError() +
-                        Math.min(((VariantBackedByGenotype)parent1).getCalledGenotype().getNegLog10PError(),
-                                 ((VariantBackedByGenotype)parent2).getCalledGenotype().getNegLog10PError()));
+                    double sumConfidences = 0.5 * (0.5 * child.getNegLog10PError() +
+                            Math.min(parent1.getNegLog10PError(), parent2.getNegLog10PError()));
 
-                out.format("%s\t", child.getLocation().getContig());
-                out.format("%s\t", child.getLocation().getStart());
-                out.format("%.4f\t", sumConfidences);
-                out.format("%.4f\t", child.getNegLog10PError());
-                out.format("%.4f\t", ((VariantBackedByGenotype)parent1).getCalledGenotype().getNegLog10PError());
-                out.format("%.4f\t", ((VariantBackedByGenotype)parent2).getCalledGenotype().getNegLog10PError());
-                out.format("%s\t", dbsnp != null);
+                    out.format("%s\t", child.getLocation().getContig());
+                    out.format("%s\t", child.getLocation().getStart());
+                    out.format("%.4f\t", sumConfidences);
+                    out.format("%.4f\t", child.getNegLog10PError());
+                    out.format("%.4f\t", parent1.getNegLog10PError());
+                    out.format("%.4f\t", parent2.getNegLog10PError());
+                    out.format("%s\t", dbsnp != null);
 
-                out.format ("%s\t", child.toString());
-                out.format ("%s\t", parent1.toString());
-                out.format ("%s", parent2.toString());
-                if (dbsnp != null)
-                    out.format ("\tDBSNP\t:%s", dbsnp.toString());
-                out.println();
+                    out.format ("%s\t", child.toString());
+                    out.format ("%s\t", parent1.toString());
+                    out.format ("%s", parent2.toString());
+                    if (dbsnp != null)
+                        out.format ("\tDBSNP\t:%s", dbsnp.toString());
+                    out.println();
+                }
             }
         }
 
@@ -67,5 +113,5 @@ public class DeNovoSNPWalker extends RefWalker<String, Integer>{
         return 1;
     }
 
-
+    public void onTraversalDone(Integer result) {} // Don't print the reduce result
 }