diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index 7c9753a78..525df67fb 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -73,11 +73,12 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
      *
      * @return reference allele, forward strand
      */
- public String getRefBasesFWD() {
-        if ( onFwdStrand() )
-            return refBases;
-        else
-            return SequenceUtil.reverseComplement(refBases);
+    public String getRefBasesFWD() {
+        return getAllelesFWD().get(0);
+        //if ( onFwdStrand() )
+        //    return refBases;
+        //else
+        //    return SequenceUtil.reverseComplement(refBases);
     }
 
     /**
@@ -87,9 +88,11 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
      * @return reference base on the forward strand
      */
     public char getRefSnpFWD() throws IllegalStateException {
+        //System.out.printf("refbases is %s but %s%n", refBases, toString());
         if ( isIndel() ) throw new IllegalStateException("Variant is not a SNP");
-        if ( onFwdStrand() ) return refBases.charAt(0);
-        else return SequenceUtil.reverseComplement(refBases).charAt(0);
+        return getAllelesFWD().get(0).charAt(0);
+        // if ( onFwdStrand() ) return refBases.charAt(0);
+       // else return SequenceUtil.reverseComplement(refBases).charAt(0);
     }
 
     public List<String> getAllelesFWD() {
@@ -187,8 +190,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 
 	@Override
 	public char getAltSnpFWD() throws IllegalStateException {
-		// TODO Auto-generated method stub
-		return 0;
+        return getAllelesFWD().get(1).charAt(0);
 	}
 
 	@Override
@@ -205,8 +207,8 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 
 	@Override
 	public double getMAF() {
-		// TODO Auto-generated method stub
-		return 0;
+		// Fixme: update to actually get MAF 
+		return avHet;
 	}
 
 	@Override
@@ -218,7 +220,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 	@Override
 	public double getVariationConfidence() {
 		// TODO Auto-generated method stub
-		return 0;
+		return 100;
 	}
 
 	@Override
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicateQualsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicateQualsWalker.java
index f3c7472c4..32111633f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicateQualsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicateQualsWalker.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.duplicates.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;
diff --git a/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index 376e1d8a1..faa97533c 100644
--- a/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -6,6 +6,38 @@ package org.broadinstitute.sting.utils;
  * @author Kiran Garimella
  */
 public class BaseUtils {
+
+    /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
+    // a pyrimidine to another pyrimidine nucleotide (C <-> T).
+    // Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions.
+    public enum BaseSubstitutionType {
+        TRANSITION,         // A <-> G or C <-> T
+        TRANSVERSION
+    }
+
+    /**
+     * Returns the base substitution type of the 2 state SNP
+     * @param base1
+     * @param base2
+     * @return
+     */
+    public static BaseSubstitutionType SNPSubstitutionType( char base1, char base2 ) {
+        BaseSubstitutionType t = isTransition(base1, base2) ? BaseSubstitutionType.TRANSITION : BaseSubstitutionType.TRANSVERSION;
+        //System.out.printf("SNPSubstitutionType( char %c, char %c ) => %s%n", base1, base2, t);
+        return t;
+    }
+
+    public static boolean isTransition( char base1, char base2 ) {
+        int b1 = simpleBaseToBaseIndex(base1);
+        int b2 = simpleBaseToBaseIndex(base2);
+        return b1 == 0 && b2 == 2 || b1 == 2 && b2 == 0 ||
+               b1 == 1 && b2 == 3 || b1 == 3 && b2 == 1;
+    }
+
+    public static boolean isTransversion( char base1, char base2 ) {
+        return ! isTransition(base1, base2);
+    }
+
     /** Private constructor.  No instantiating this class! */
     private BaseUtils() {}
 
diff --git a/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java b/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
index 9a0d17dc7..e37ac8d5c 100755
--- a/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
+++ b/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
@@ -18,6 +18,33 @@ public class BaseUtilsTest extends BaseTest {
         compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0);
     }
 
+    @Test
+    public void testTransitionTransversion() {
+        logger.warn("Executing testTransitionTransversion");
+
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 't' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 't' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+        Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
+    }
+
     private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
         double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
         Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);