diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
index bfb18ed1c..600c1124f 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
@@ -28,7 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
 import org.broadinstitute.sting.gatk.refdata.tracks.RODRMDTrack;
-import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
 
 import java.io.File;
 import java.util.HashMap;
@@ -61,7 +60,6 @@ public class RODTrackBuilder implements RMDTrackBuilder {
         Types.put("Intervals", IntervalRod.class);
         Types.put("GLF", RodGLF.class);
         Types.put("PicardDbSNP", rodPicardDbSNP.class);
-        Types.put("HapmapVCF", HapmapVCFROD.class);
         Types.put("Beagle", BeagleROD.class);
         Types.put("Plink", PlinkRod.class);        
     }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java b/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
deleted file mode 100644
index d68c00265..000000000
--- a/java/src/org/broadinstitute/sting/oneoffprojects/refdata/HapmapVCFROD.java
+++ /dev/null
@@ -1,147 +0,0 @@
-package org.broadinstitute.sting.oneoffprojects.refdata;
-
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFRecord;
-import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.Iterator;
-import java.util.List;
-
-/*
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: Jan 29, 2010
- */
-public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Iterator<HapmapVCFROD> {
-// This is a (hopefully temporary) wrapper class for certain VCF files that we want to protect from
-// utilities that grab genotypes or sample names across all VCF files
-
-    private VCFRecord record;
-    private VCFReader reader;
-
-    public VCFReader getReader() {
-        return reader;
-    }
-
-    public VCFRecord getRecord() {
-        return record;
-    }
-
-    public HapmapVCFROD(String name) {
-        super(name);
-    }
-
-    public HapmapVCFROD(String name, VCFRecord currentRecord, VCFReader reader) {
-        super(name);
-        this.record = currentRecord;
-        this.reader = reader;
-    }
-
-    public Object initialize(final File source) throws FileNotFoundException {
-        reader = new VCFReader(source);
-        if (reader.hasNext()) record = reader.next();
-        return reader.getHeader();
-    }
-
-    public boolean parseLine(Object obj, String[] args) {
-        return false;
-    }
-
-    public double getNegLog10PError() {
-        return record.getNegLog10PError();
-    }
-    public String getReference() {
-        return record.getReference();
-    }
-
-    public String toString() {
-        return record.toString();
-    }
-
-    public List<String> getAlternateAlleleList() {
-        return record.getAlternateAlleleList();
-    }
-
-    public boolean isDeletion() {
-        return record.isDeletion();
-    }
-
-    public GenomeLoc getLocation() {
-        return GenomeLocParser.createGenomeLoc(record.getChr(),record.getStart());
-    }
-
-    public boolean isBiallelic() {
-        return record.isBiallelic();
-    }
-
-    public boolean isIndel() {
-        return record.isIndel();
-    }
-
-    public boolean isSNP() {
-        return record.isSNP();
-    }
-
-    public boolean isReference() {
-        return record.isReference();
-    }
-
-    public double getNonRefAlleleFrequency() {
-        return record.getNonRefAlleleFrequency();
-    }
-
-    public char getAlternativeBaseForSNP() {
-        return record.getAlternativeBaseForSNP();
-    }
-
-    public boolean isInsertion() {
-        return record.isInsertion();
-    }
-
-    public List<String> getAlleleList() {
-        return record.getAlleleList();
-    }
-
-    public char getReferenceForSNP() {
-        return record.getReferenceForSNP();
-    }
-
-    public boolean hasGenotype(DiploidGenotype g) {
-        return false;
-        //return rod.hasGenotype(g);
-    }
-
-    public VCFHeader getHeader() {
-        return record.getHeader();
-    }
-
-    public boolean hasNext() {
-        return reader.hasNext();
-    }
-
-    public HapmapVCFROD next() {
-        return new HapmapVCFROD(name, record, reader);
-    }
-
-    public void remove() {
-        throw new UnsupportedOperationException("Unable to remove");
-    }
-
-    public static HapmapVCFROD createIterator(String name, File file) {
-        HapmapVCFROD vcf = new HapmapVCFROD(name);
-        try {
-            vcf.initialize(file);
-        } catch (FileNotFoundException e) {
-            throw new StingException("Unable to load file",e);
-        }
-        return vcf;
-    }
-
-}
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java
index fd85bdda6..994d75fe7 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
 
 import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broad.tribble.vcf.VCFRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -34,17 +34,17 @@ public class ThousandGenomesAnnotator implements InfoFieldAnnotation {
         if ( tracker == null )
             return null;
 
-        HapmapVCFROD pilot1 = tracker.lookup("pilot1",HapmapVCFROD.class);
-        HapmapVCFROD pilot2 = tracker.lookup("pilot2",HapmapVCFROD.class);
+        VCFRecord pilot1 = tracker.lookup("pilot1", VCFRecord.class);
+        VCFRecord pilot2 = tracker.lookup("pilot2", VCFRecord.class);
 
         String result;
 
         if ( pilot1 == null && pilot2 == null) {
             result = "0";
         } else {
-            if ( pilot1 != null && ! pilot1.getRecord().isFiltered() ) {
+            if ( pilot1 != null && ! pilot1.isFiltered() ) {
                 result = "1";
-            } else if ( pilot2 != null && !pilot2.getRecord().isFiltered() ) {
+            } else if ( pilot2 != null && !pilot2.isFiltered() ) {
                 result = "1";
             } else {
                 result = "0";