diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
index ec1d5ecb1..7181d1988 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
@@ -4,11 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
-import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.HashMap;
@@ -108,26 +104,19 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
             // First find out if this variant is in the truth sets
             boolean isInTruthSet = false;
             boolean isTrueVariant = false;
-            for( final GATKFeature feature : tracker.getAllRods() ) {
-                Object rod = feature.getUnderlyingObject();
-                if( rod != null && feature.getName().toUpperCase().startsWith("TRUTH") ) {
+            for ( VariantContext vc : tracker.getAllVariantContexts() ) {
+                if( vc.getName().toUpperCase().startsWith("TRUTH") ) {
                     isInTruthSet = true;
-                    VariantContext variantContext = VariantContextAdaptors.toVariantContext(feature.getName(),rod);
-                    // First check that the conversion to VC worked correctly; next see if the truth sets say this site is variant or reference
-                    if (variantContext == null)
-                        throw new StingException("Truth ROD is of type that can't be converted to a VariantContext ( type = " + feature.getName() + ")");
-                    else if (variantContext.isSNP())
+                    if (vc.isVariant())
                         isTrueVariant = true;
                 }
             }
             
             // Add each annotation in this VCF Record to the dataManager
-            for( final GATKFeature feature : tracker.getAllRods() ) {
-                Object rod = feature.getUnderlyingObject();
-                if( rod != null && rod instanceof RodVCF && !feature.getName().toUpperCase().startsWith("TRUTH") ) {
-                    final RodVCF variant = (RodVCF) rod;
-                    if( variant.isSNP() ) {
-                        dataManager.addAnnotations( variant, SAMPLE_NAME, isInTruthSet, isTrueVariant );
+            for ( VariantContext vc : tracker.getAllVariantContexts() ) {
+                if( !vc.getName().toUpperCase().startsWith("TRUTH") ) {
+                    if( vc.isVariant() ) {
+                        dataManager.addAnnotations( vc, ref.getBase(), SAMPLE_NAME, isInTruthSet, isTrueVariant );
                     }
                 }
             }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
index 8d76b24a8..43e6058bc 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
@@ -1,8 +1,10 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
+import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
 
 import java.util.*;
 import java.io.IOException;
@@ -52,14 +54,16 @@ public class AnnotationDataManager {
         INDICATE_MEAN_NUM_VARS = _INDICATE_MEAN_NUM_VARS;
     }
 
-    public void addAnnotations( final RodVCF variant, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
+    public void addAnnotations( final VariantContext vc, final char ref, final String sampleName, final boolean isInTruthSet, final boolean isTrueVariant ) {
 
         if( sampleName != null ) { // Only process variants that are found in the sample with this sampleName
-            if( variant.getGenotype(sampleName).isNoCall() ) { // This variant isn't found in this sample so break out
+            if( vc.getGenotype(sampleName).isNoCall() ) { // This variant isn't found in this sample so break out
                 return;
             }
         } // else, process all samples
 
+        VCFRecord variant = VariantContextAdaptors.toVCF(vc, ref);
+
         // Loop over each annotation in the vcf record
         final Map<String,String> infoField = variant.getInfoValues();
         infoField.put("QUAL", ((Double)variant.getQual()).toString() ); // add QUAL field to annotations
@@ -87,10 +91,12 @@ public class AnnotationDataManager {
             final boolean isNovelVariant = variant.getID().equals(".");
 
             // Decide if the variant is a transition or transversion
-            if( BaseUtils.isTransition( (byte)variant.getReferenceForSNP(), (byte)variant.getAlternativeBaseForSNP()) ) {
-                datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant );
-            } else {
-                datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );
+            if ( vc.isSNP() ) {
+                if( BaseUtils.isTransition( vc.getReference().getBases()[0], vc.getAlternateAllele(0).getBases()[0]) ) {
+                    datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant );
+                } else {
+                    datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );
+                }
             }
         }
     }