diff --git a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotypeBackedVariation.java b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotypeBackedVariation.java
deleted file mode 100755
index f73997711..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotypeBackedVariation.java
+++ /dev/null
@@ -1,188 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.util.*;
-
-/**
- * @author ebanks
- *         <p/>
- *         Class BasicGenotypeBackedVariation
- *         <p/>
- *         represents a genotype-backed Variation.
- */
-public class BasicGenotypeBackedVariation implements Variation, VariantBackedByGenotype {
-
-    // the discovery lod score
-    private double mConfidence = 0.0;
-
-    // the location
-    private GenomeLoc mLoc;
-
-    // the ref base and alt bases
-    private char mRefBase;
-    private List<String> mAltBases = new ArrayList<String>();
-
-    // the variant type
-    private final VARIANT_TYPE mType = VARIANT_TYPE.SNP;
-
-    // the genotypes
-    private List<Genotype> mGenotypes = null;
-
-
-    /**
-     * create a basic genotype-backed variation bject, given the following fields
-     *
-     * @param ref       the reference base
-     * @param loc       the locus
-     * @param type      the variant type
-     */
-    public BasicGenotypeBackedVariation(char ref, GenomeLoc loc, VARIANT_TYPE type) {
-        if ( type != VARIANT_TYPE.SNP && type != VARIANT_TYPE.REFERENCE )
-            throw new IllegalArgumentException("Only SNPs and REFs are supported in the Geli format");
-        mRefBase = ref;
-        mLoc = loc;
-    }
-
-    /**
-      * get the reference base.
-      * @return a character, representing the reference base
-      */
-    public String getReference() {
-        return String.valueOf(mRefBase);
-    }
-
-    /**
-     * get the genotype's location
-     *
-     * @return a GenomeLoc representing the location
-     */
-    public GenomeLoc getLocation() {
-        return mLoc;
-    }
-
-    public boolean isBiallelic() {
-        return true;
-    }
-
-    public boolean isSNP() {
-        return mType == VARIANT_TYPE.SNP;
-    }
-
-    public boolean isInsertion() {
-        return false;
-    }
-
-    public boolean isIndel() {
-        return false;
-    }
-
-    public boolean isDeletion() {
-        return false;
-    }
-
-    public boolean isReference() {
-        return mType == VARIANT_TYPE.REFERENCE;
-    }
-
-    public VARIANT_TYPE getType() {
-        return mType;
-    }
-
-    public double getNegLog10PError() {
-        return mConfidence / 10.0;
-    }
-
-    public double getNonRefAlleleFrequency() {
-        return 0.0;
-    }
-
-    public List<String> getAlternateAlleleList() {
-        return mAltBases;
-    }
-
-    public void addAlternateAllele(String alt) {
-        mAltBases.add(alt);
-    }
-
-    public List<String> getAlleleList() {
-        LinkedList<String> alleles = new LinkedList<String>(mAltBases);
-        alleles.addFirst(getReference());
-        return alleles;
-    }
-
-    public char getAlternativeBaseForSNP() {
-        if ( !isSNP() )
-            throw new IllegalStateException("This variant is not a SNP");
-        if ( mAltBases.size() == 0 )
-            throw new IllegalStateException("No alternate alleles have been set");
-        return mAltBases.get(0).charAt(0);
-    }
-
-    public char getReferenceForSNP() {
-        if ( !isSNP() )
-            throw new IllegalStateException("This variant is not a SNP");
-        return mRefBase;
-    }
-
-    /**
-     * get the confidence
-     *
-     * @return the confidence
-     */
-    public double getConfidence() {
-        return mConfidence;
-    }
-
-    /**
-     *
-     * @param   confidence    the confidence for this genotype
-     */
-    public void setConfidence(double confidence) {
-        mConfidence = confidence;
-    }
-
-    /**
-     *
-     * @param   calls    the GenotypeCalls for this variation
-     */
-    public void setGenotypeCalls(List<Genotype> calls) {
-        mGenotypes = calls;
-    }
-
-    /**
-     * @return a specific genotype that represents the called genotype
-     */
-    public Genotype getCalledGenotype() {
-        if ( mGenotypes == null || mGenotypes.size() != 1 )
-            throw new IllegalStateException("There is not one and only one Genotype associated with this Variation");
-        return mGenotypes.get(0);
-    }
-
-    /**
-     * @return a list of all the genotypes
-     */
-    public List<Genotype> getGenotypes() {
-        return mGenotypes;
-    }
-
-    /**
-     * do we have the specified genotype?  not all backedByGenotypes
-     * have all the genotype data.
-     *
-     * @param x the genotype
-     *
-     * @return true if available, false otherwise
-     */
-    public boolean hasGenotype(DiploidGenotype x) {
-        if ( mGenotypes == null )
-            return false;
-
-        for ( Genotype g : mGenotypes ) {
-            if ( DiploidGenotype.valueOf(g.getBases()).equals(x) )
-                return true;
-        }
-
-        return false;
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LexigraphicalComparator.java b/java/src/org/broadinstitute/sting/utils/genotype/LexigraphicalComparator.java
deleted file mode 100644
index 6568bc22a..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/LexigraphicalComparator.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-import java.util.Comparator;
-
-
-/**
- * 
- * @author aaron 
- * 
- * Class LexigraphicalComparator
- *
- * A descriptions should go here. Blame aaron if it's missing.
- */
-
-public class LexigraphicalComparator implements Comparator<Genotype> {
-    private final Double EPSILON = 1.0e-15;
-
-    @Override
-    public int compare(Genotype genotype, Genotype genotype1) {
-        return genotype.getBases().compareTo(genotype1.getBases());
-    }
-}