diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 96a400c68..971727727 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -86,6 +86,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
 
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
+    public RodBinding<VariantContext> getVariantRodBinding() { return variantCollection.variants; }
 
     /**
      * The INFO field will be annotated with information on the most biologically-significant effect
@@ -208,6 +209,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
             engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, this);
         engine.initializeExpressions(expressionsToUse);
 
+        engine.invokeAnnotationInitializationMethods();
+
         // setup the header fields
         // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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 01926a7f3..17830f129 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
@@ -29,10 +29,7 @@ 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.annotator.interfaces.AnnotationInterfaceManager;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+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;
@@ -113,6 +110,16 @@ public class VariantAnnotatorEngine {
             dbAnnotations.put(rod, rod.getName());
     }
 
+    public void invokeAnnotationInitializationMethods() {
+        for ( VariantAnnotatorAnnotation annotation : requestedInfoAnnotations ) {
+            annotation.initialize(walker);
+        }
+
+        for ( VariantAnnotatorAnnotation annotation : requestedGenotypeAnnotations ) {
+            annotation.initialize(walker);
+        }
+    }
+
     public Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
 
         Set<VCFHeaderLine> descriptions = new HashSet<VCFHeaderLine>();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
index 20a2aea0e..9dda57ae3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
@@ -9,6 +9,7 @@ import java.util.List;
 public interface AnnotatorCompatibleWalker {
 
     // getter methods for various used bindings
+    public abstract RodBinding<VariantContext> getVariantRodBinding();
     public abstract RodBinding<SnpEffFeature> getSnpEffRodBinding();
     public abstract RodBinding<VariantContext> getDbsnpRodBinding();
     public abstract List<RodBinding<VariantContext>> getCompRodBindings();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
index f33d61df9..9e48de9c3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
@@ -24,18 +24,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
-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.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
-import java.util.Map;
 
 @DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
 public abstract class VariantAnnotatorAnnotation {
     // return the INFO keys
     public abstract List<String> getKeyNames();
+
+    // initialization method (optional for subclasses, and therefore non-abstract)
+    public void initialize ( AnnotatorCompatibleWalker walker ) { }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index d5dbdedd6..4ee2d5f44 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -127,6 +127,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     @ArgumentCollection
     protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
     public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
+    public RodBinding<VariantContext> getVariantRodBinding() { return null; }
     public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
     public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
     public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }