diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index 97a4ac468..6eea12e2b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -5,12 +5,10 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
+import java.util.*;
 
 
 /**
@@ -31,8 +29,31 @@ public class BaseQualityRankSumTest extends RankSumTest {
                     altQuals.add((double)p.getQual());
             }
         }
-
     }
+    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) {
+        // TODO -- implement me; how do we pull out the correct offset from the read?
+        return;
+
+/*
+        for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
+            final boolean matchesRef = ref.equals(alleleBin.getKey());
+            final boolean matchesAlt = alts.contains(alleleBin.getKey());
+            if ( !matchesRef && !matchesAlt )
+                continue;
+
+            for ( final GATKSAMRecord read : alleleBin.getValue() ) {
+
+                if ( isUsableBase(p) ) {
+                    if ( matchesRef )
+                        refQuals.add((double)p.getQual());
+                    else
+                        altQuals.add((double)p.getQual());
+                }
+            }
+        }
+*/
+    }
+
     protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
         HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index 0acd3e841..b3a8dbebd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@@ -35,6 +36,8 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
@@ -49,7 +52,7 @@ import java.util.Map;
  * allele Frequency, for each ALT allele, in the same order as listed; total number
  * of alleles in called genotypes.
  */
-public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation {
+public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
     private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
@@ -63,6 +66,13 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
         return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap<String, Object>(), true);
     }
 
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        if ( ! vc.hasGenotypes() )
+            return null;
+
+        return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap<String, Object>(), true);
+    }
+
     public List<String> getKeyNames() {
         return Arrays.asList(keyNames);
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index b744fec46..f94d48893 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -3,12 +3,15 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
@@ -33,7 +36,7 @@ import java.util.Map;
  * Note that the DP is affected by downsampling (-dcov) though, so the max value one can obtain for N samples with
  * -dcov D is N * D
  */
-public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation {
+public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
@@ -47,6 +50,22 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
         return map;
     }
 
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
+        int depth = 0;
+        for ( final Map<Allele, List<GATKSAMRecord>> alleleBins : stratifiedContexts.values() ) {
+            for ( final List<GATKSAMRecord> alleleBin : alleleBins.values() ) {
+                depth += alleleBin.size();
+            }
+        }
+
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(getKeyNames().get(0), String.format("%d", depth));
+        return map;
+    }
+
     public List<String> getKeyNames() { return Arrays.asList(VCFConstants.DEPTH_KEY); }
 
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Approximate read depth; some reads may have been filtered")); }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 817d6b1ff..0d3bd11a7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -28,6 +28,7 @@ import cern.jet.math.Arithmetic;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@@ -37,6 +38,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
@@ -49,7 +51,7 @@ import java.util.*;
  * indicative of false positive calls.  Note that the fisher strand test may not be
  * calculated for certain complex indel cases or for multi-allelic sites.
  */
-public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation {
+public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
     private static final String FS = "FS";
     private static final double MIN_PVALUE = 1E-320;
 
@@ -78,6 +80,22 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
         return map;
     }
 
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        if ( !vc.isVariant() )
+            return null;
+
+        int[][] table = getContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
+
+        Double pvalue = Math.max(pValueForContingencyTable(table), MIN_PVALUE);
+        if ( pvalue == null )
+            return null;
+
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pvalue)));
+        return map;
+
+    }
+
     public List<String> getKeyNames() {
         return Arrays.asList(FS);
     }
@@ -193,6 +211,38 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
         return sum;
     }
 
+    /**
+     Allocate and fill a 2x2 strand contingency table.  In the end, it'll look something like this:
+     *             fw      rc
+     *   allele1   #       #
+     *   allele2   #       #
+     * @return a 2x2 contingency table
+     */
+    private static int[][] getContingencyTable(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, Allele ref, Allele alt) {
+        int[][] table = new int[2][2];
+
+        for ( final Map<Allele, List<GATKSAMRecord>> alleleBins : stratifiedContexts.values() ) {
+            for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : alleleBins.entrySet() ) {
+
+                final boolean matchesRef = ref.equals(alleleBin.getKey());
+                final boolean matchesAlt = alt.equals(alleleBin.getKey());
+                if ( !matchesRef && !matchesAlt )
+                    continue;
+
+                for ( final GATKSAMRecord read : alleleBin.getValue() ) {
+                    boolean isFW = read.getReadNegativeStrandFlag();
+
+                    int row = matchesRef ? 0 : 1;
+                    int column = isFW ? 0 : 1;
+
+                    table[row][column]++;
+                }
+            }
+        }
+
+        return table;
+    }
+
     /**
      Allocate and fill a 2x2 strand contingency table.  In the end, it'll look something like this:
      *             fw      rc
@@ -214,8 +264,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
                 Allele base = Allele.create(p.getBase(), false);
                 boolean isFW = !p.getRead().getReadNegativeStrandFlag();
 
-                boolean matchesRef = ref.equals(base, true);
-                boolean matchesAlt = alt.equals(base, true);
+                final boolean matchesRef = ref.equals(base, true);
+                final boolean matchesAlt = alt.equals(base, true);
                 if ( matchesRef || matchesAlt ) {
                     int row = matchesRef ? 0 : 1;
                     int column = isFW ? 0 : 1;
@@ -227,6 +277,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
         return table;
     }
+
     /**
      Allocate and fill a 2x2 strand contingency table.  In the end, it'll look something like this:
      *             fw      rc
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index 6366890d5..57561a277 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -3,12 +3,15 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -27,12 +30,19 @@ import java.util.Map;
  * more information.  Note that the Inbreeding Coefficient will not be calculated for files
  * with fewer than a minimum (generally 10) number of samples.
  */
-public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation {
+public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     private static final int MIN_SAMPLES = 10;
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+        return calculateIC(vc);
+    }
 
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        return calculateIC(vc);
+    }
+
+    private Map<String, Object> calculateIC(final VariantContext vc) {
         final GenotypesContext genotypes = vc.getGenotypes();
         if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
             return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index aa4f26ef3..520b0f232 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -6,12 +6,10 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
+import java.util.*;
 
 
 /**
@@ -35,6 +33,23 @@ public class MappingQualityRankSumTest extends RankSumTest {
             }
         }
     }
+
+    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) {
+        for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
+            final boolean matchesRef = ref.equals(alleleBin.getKey());
+            final boolean matchesAlt = alts.contains(alleleBin.getKey());
+            if ( !matchesRef && !matchesAlt )
+                continue;
+
+            for ( final GATKSAMRecord read : alleleBin.getValue() ) {
+                if ( matchesRef )
+                    refQuals.add((double)read.getMappingQuality());
+                else
+                    altQuals.add((double)read.getMappingQuality());
+            }
+        }
+    }
+
     protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
         HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index bf60dec6b..24a107235 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -3,11 +3,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -23,7 +26,7 @@ import java.util.Map;
  * Low scores are indicative of false positive calls and artifacts.  Note that QualByDepth requires sequencing
  * reads associated with the samples with polymorphic genotypes.
  */
-public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation {
+public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
@@ -62,4 +65,40 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
 
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth")); }
 
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
+        final GenotypesContext genotypes = vc.getGenotypes();
+        if ( genotypes == null || genotypes.size() == 0 )
+            return null;
+
+        int depth = 0;
+
+        for ( final Genotype genotype : genotypes ) {
+
+            // we care only about variant calls with likelihoods
+            if ( !genotype.isHet() && !genotype.isHomVar() )
+                continue;
+
+            final Map<Allele, List<GATKSAMRecord>> alleleBins = stratifiedContexts.get(genotype.getSampleName());
+            if ( alleleBins == null )
+                continue;
+
+            for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : alleleBins.entrySet() ) {
+                if ( !alleleBin.getKey().equals(Allele.NO_CALL) )
+                    depth += alleleBin.getValue().size();
+            }
+        }
+
+        if ( depth == 0 )
+            return null;
+
+        double QD = -10.0 * vc.getLog10PError() / (double)depth;
+
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(getKeyNames().get(0), String.format("%.2f", QD));
+        return map;
+    }
+
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 50ade5334..97c15e747 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@@ -13,6 +14,8 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
@@ -24,7 +27,7 @@ import java.util.Map;
 /**
  * Root Mean Square of the mapping quality of the reads across all samples.
  */
-public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation {
+public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
@@ -34,7 +37,7 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn
         for ( AlignmentContext context : stratifiedContexts.values() )
             totalSize += context.size();
 
-        int[] qualities = new int[totalSize];
+        final int[] qualities = new int[totalSize];
         int index = 0;
 
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
@@ -54,6 +57,35 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn
         return map;
     }
 
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
+        int depth = 0;
+        for ( final Map<Allele, List<GATKSAMRecord>> alleleBins : stratifiedContexts.values() ) {
+            for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : alleleBins.entrySet() ) {
+                depth += alleleBin.getValue().size();
+            }
+        }
+
+        final int[] qualities = new int[depth];
+        int index = 0;
+
+        for ( final Map<Allele, List<GATKSAMRecord>> alleleBins : stratifiedContexts.values() ) {
+            for ( final List<GATKSAMRecord> reads : alleleBins.values() ) {
+                for ( final GATKSAMRecord read : reads ) {
+                    if ( read.getMappingQuality() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE )
+                        qualities[index++] = read.getMappingQuality();
+                }
+            }
+        }
+
+        double rms = MathUtils.rms(qualities);
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(getKeyNames().get(0), String.format("%.2f", rms));
+        return map;
+    }
+
     public List<String> getKeyNames() { return Arrays.asList(VCFConstants.RMS_MAPPING_QUALITY_KEY); }
 
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "RMS Mapping Quality")); }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index ff5f8f144..80d248ac2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 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.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@@ -12,6 +13,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
@@ -26,7 +28,7 @@ import java.util.Map;
 /**
  * Abstract root for all RankSum based annotations
  */
-public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation {
+public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
     static final double INDEL_LIKELIHOOD_THRESH = 0.1;
     static final boolean DEBUG = false;
 
@@ -38,7 +40,6 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         if (genotypes == null || genotypes.size() == 0)
             return null;
 
-
         final ArrayList<Double> refQuals = new ArrayList<Double>();
         final ArrayList<Double> altQuals = new ArrayList<Double>();
 
@@ -104,12 +105,52 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         if (!Double.isNaN(testResults.first))
             map.put(getKeyNames().get(0), String.format("%.3f", testResults.first));
         return map;
-
     }
 
-    protected abstract void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
+    public Map<String, Object> annotate(Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        if (stratifiedContexts.size() == 0)
+            return null;
 
-    protected abstract void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
+        final GenotypesContext genotypes = vc.getGenotypes();
+        if (genotypes == null || genotypes.size() == 0)
+            return null;
+
+        final ArrayList<Double> refQuals = new ArrayList<Double>();
+        final ArrayList<Double> altQuals = new ArrayList<Double>();
+
+        for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
+            final Map<Allele, List<GATKSAMRecord>> context = stratifiedContexts.get(genotype.getSampleName());
+            if ( context == null )
+                continue;
+
+            fillQualsFromPileup(vc.getReference(), vc.getAlternateAlleles(), context, refQuals, altQuals);
+        }
+
+        if ( refQuals.size() == 0 || altQuals.size() == 0 )
+            return null;
+
+        final MannWhitneyU mannWhitneyU = new MannWhitneyU();
+        for (final Double qual : altQuals) {
+            mannWhitneyU.add(qual, MannWhitneyU.USet.SET1);
+        }
+        for (final Double qual : refQuals) {
+            mannWhitneyU.add(qual, MannWhitneyU.USet.SET2);
+        }
+
+        // we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases)
+        final Pair<Double, Double> testResults = mannWhitneyU.runOneSidedTest(MannWhitneyU.USet.SET1);
+
+        final Map<String, Object> map = new HashMap<String, Object>();
+        if (!Double.isNaN(testResults.first))
+            map.put(getKeyNames().get(0), String.format("%.3f", testResults.first));
+        return map;
+    }
+
+    protected abstract void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals);
+
+    protected abstract void fillQualsFromPileup(final byte ref, final List<Byte> alts, final ReadBackedPileup pileup, final List<Double> refQuals, final List<Double> altQuals);
+
+    protected abstract void fillIndelQualsFromPileup(final ReadBackedPileup pileup, final List<Double> refQuals, final List<Double> altQuals);
 
     protected static boolean isUsableBase(final PileupElement p) {
         return !(p.isInsertionAtBeginningOfRead() ||
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index a998cd08b..e013f0e08 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -11,12 +11,10 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
+import java.util.*;
 
 /**
  * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error).
@@ -49,6 +47,27 @@ public class ReadPosRankSumTest extends RankSumTest {
         }
     }
 
+    protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) {
+        // TODO -- implement me; how do we pull out the correct offset from the read?
+        return;
+
+/*
+        for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
+            final boolean matchesRef = ref.equals(alleleBin.getKey());
+            final boolean matchesAlt = alts.contains(alleleBin.getKey());
+            if ( !matchesRef && !matchesAlt )
+                continue;
+
+            for ( final GATKSAMRecord read : alleleBin.getValue() ) {
+                if ( matchesRef )
+                    refQuals.add((double)read.getMappingQuality());
+                else
+                    altQuals.add((double)read.getMappingQuality());
+            }
+        }
+*/
+    }
+
     protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele
         // to classify a pileup element as ref or alt, we look at the likelihood associated with the allele associated to this element.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 90d0ad740..413c32a24 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -33,10 +33,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
@@ -94,6 +92,13 @@ public class VariantAnnotatorEngine {
         initializeDBs();
     }
 
+    // experimental constructor for active region traversal
+    public VariantAnnotatorEngine(GenomeAnalysisEngine toolkit) {
+        this.walker = null;
+        this.toolkit = toolkit;
+        requestedInfoAnnotations = AnnotationInterfaceManager.createInfoFieldAnnotations(Arrays.asList("ActiveRegionBasedAnnotation"), Collections.<String>emptyList());
+    }
+
     // select specific expressions to use
     public void initializeExpressions(List<String> expressionsToUse) {
         // set up the expressions
@@ -169,7 +174,7 @@ public class VariantAnnotatorEngine {
         this.requireStrictAlleleMatch = requireStrictAlleleMatch;
     }
 
-    public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public VariantContext annotateContext(final RefMetaDataTracker tracker, final ReferenceContext ref, final Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes());
 
         // annotate db occurrences
@@ -192,6 +197,20 @@ public class VariantAnnotatorEngine {
         return builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc)).make();
     }
 
+    public VariantContext annotateContext(final Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, VariantContext vc) {
+        Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes());
+
+        // go through all the requested info annotationTypes
+        for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
+            Map<String, Object> annotationsFromCurrentType = ((ActiveRegionBasedAnnotation)annotationType).annotate(stratifiedContexts, vc);
+            if ( annotationsFromCurrentType != null )
+                infoAnnotations.putAll(annotationsFromCurrentType);
+        }
+
+        // generate a new annotated VC
+        return new VariantContextBuilder(vc).attributes(infoAnnotations).make();
+    }
+
     private VariantContext annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
         for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
             if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
index 2c1bb0974..de61c7741 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
@@ -9,7 +9,7 @@ import java.util.List;
 import java.util.Map;
 
 // TODO -- make this an abstract class when we move away from InfoFieldAnnotation
-public interface ActiveRegionBasedAnnotation {
+public interface ActiveRegionBasedAnnotation extends AnnotationType {
     // return annotations for the given contexts split by sample and then allele
     public abstract Map<String, Object> annotate(final Map<String, Map<Allele, List<GATKSAMRecord>>> stratifiedContexts, final VariantContext vc);