diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
index 0027ecee0..6126fbd16 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
@@ -30,9 +30,6 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.Utils;
 import org.apache.log4j.Logger;
 
 import java.util.*;
@@ -70,64 +67,8 @@ public class VCFUtils {
         return fields;
     }
 
-    /**
-     * Merges various vcf records into a single one using the mapping from rodNamesToSampleNames to get unique sample names
-     *
-     * @param rods                   the vcf rods
-     * @param rodNamesToSampleNames  mapping of rod/sample pairs to new uniquified sample names
-     * @return the new merged vcf record
-     */
-    public static VCFRecord mergeRecords(Map<VCFRecord,String> rods, Map<Pair<String, String>, String> rodNamesToSampleNames) {
-
-        VCFParameters params = new VCFParameters();
-        params.addFormatItem(VCFConstants.GENOTYPE_KEY);
-
-        // keep track of the data so we can merge them intelligently
-        double maxConfidence = 0.0;
-        String id = null;
-        Map<String, String> infoFields = new HashMap<String, String>();
-        List<String> filters = new ArrayList<String>();
-
-        for ( VCFRecord rod : rods.keySet() ) {
-            List<VCFGenotypeRecord> myGenotypes = rod.getVCFGenotypeRecords();
-            for ( VCFGenotypeRecord call : myGenotypes ) {
-                // set the name to be the new uniquified name and add it to the list of genotypes
-                call.setSampleName(rodNamesToSampleNames.get(new Pair<String, String>(rods.get(rod), call.getSampleName())));
-                if ( params.getPosition() < 1 )
-                    params.setLocations(GenomeLocParser.createGenomeLoc(rod.getChr(), rod.getStart()), call.getReference());
-                params.addGenotypeRecord(createVCFGenotypeRecord(params, call, rod));
-            }
-
-            // set the overall confidence to be the max entry we see
-            double confidence = 10.0 * rod.getNegLog10PError();
-            if ( confidence > maxConfidence )
-                maxConfidence = confidence;
-
-            if ( rod.getID() != null )
-                id = rod.getID();
-
-            if ( rod.isFiltered() )
-                filters.add(rod.getFilterString());
-
-            // just take the last value we see for a given key
-            infoFields.putAll(rod.getInfoValues());
-        }
-
-        return new VCFRecord(params.getReferenceBases(),
-                params.getContig(),
-                params.getPosition(),
-                (id != null ? id : "."),
-                params.getAlternateBases(),
-                maxConfidence,
-                filters.size() == 0 ? "0" : Utils.join(";", filters),
-                infoFields,
-                params.getFormatString(),
-                params.getGenotypeRecords());
-    }
-
     public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException {
         HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line
-        HashSet<VCFHeaderLine> lines = new HashSet<VCFHeaderLine>();
 
         // todo -- needs to remove all version headers from sources and add its own VCF version line
         for ( VCFHeader source : headers ) {
@@ -182,45 +123,4 @@ public class VCFUtils {
 
         return new HashSet<VCFHeaderLine>(map.values());
     }
-
-    /**
-     * create the VCF genotype record
-     *
-     * @param params the VCF parameters object
-     * @param gtype  the genotype
-     * @param vcfrecord  the VCF record
-     *
-     * @return a VCFGenotypeRecord
-     */
-    public static VCFGenotypeRecord createVCFGenotypeRecord(VCFParameters params, VCFGenotypeRecord gtype, VCFRecord vcfrecord) {
-
-        List<VCFGenotypeEncoding> alleles = createAlleleArray(gtype);
-        for (VCFGenotypeEncoding allele : alleles) {
-            params.addAlternateBase(allele);
-        }
-
-        VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(), alleles, VCFGenotypeRecord.PHASE.UNPHASED);
-        for ( Map.Entry<String, String> entry : gtype.getFields().entrySet() ) {
-            record.setField(entry.getKey(), entry.getValue());
-            params.addFormatItem(entry.getKey());
-        }
-
-        record.setVCFRecord(vcfrecord);
-        return record;
-    }
-
-    /**
-     * create the allele array?
-     *
-     * @param gtype the gentoype object
-     *
-     * @return a list of string representing the string array of alleles
-     */
-    private static List<VCFGenotypeEncoding> createAlleleArray(VCFGenotypeRecord gtype) {
-        List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
-        for (char allele : gtype.getBases().toCharArray()) {
-            alleles.add(new VCFGenotypeEncoding(String.valueOf(allele)));
-        }
-        return alleles;
-    }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
index ef354735b..0d604e622 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
@@ -101,26 +101,6 @@ public class VCFWriter {
         }
     }
 
-    /**
-     * output a record to the VCF file
-     *
-     * @param record                the record to output
-     */
-    @Deprecated
-    public void addRecord(VCFRecord record) {
-        if ( mHeader == null )
-            throw new IllegalStateException("The VCF Header must be written before records can be added");
-
-        String vcfString = record.toStringEncoding(mHeader);
-        try {
-            mWriter.write(vcfString + "\n");
-            mWriter.flush();  // necessary so that writing to an output stream will work
-        } catch (IOException e) {
-            throw new RuntimeException("Unable to write the VCF object to a file");
-        }
-
-    }
-
     /**
      * attempt to close the VCF file
      */