diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index 24abc4106..46a7a1972 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -71,7 +71,8 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
      * @return reference allele, forward strand
      */
     public String getRefBasesFWD() {
-        return getAllelesFWD().get(0);
+        // fix - at least this way we ensure that we'll get the other base compared to getAltBasesFWD()
+        return (getAllelesFWD().get(0).equals(refBases)) ? getAllelesFWD().get(0) : getAllelesFWD().get(1);
         //if ( onFwdStrand() )
         //    return refBases;
         //else
@@ -87,7 +88,10 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
     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");
-        return getAllelesFWD().get(0).charAt(0);
+        // fix - at least this way we ensure that we'll get the other base compared to getAltBasesFWD()
+        List<String> alleles = getAllelesFWD();
+        String val = (alleles.get(0).equals(refBases) ? alleles.get(0) : alleles.get(1));
+        return val.charAt(0);
         // if ( onFwdStrand() ) return refBases.charAt(0);
        // else return SequenceUtil.reverseComplement(refBases).charAt(0);
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java
new file mode 100644
index 000000000..8e8f21e61
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java
@@ -0,0 +1,87 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.*;
+
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class rodDbSNPTest
+ *         <p/>
+ *         A descriptions should go here. Blame aaron if it's missing.
+ */
+public class rodDbSNPTest extends BaseTest {
+    private static IndexedFastaSequenceFile seq;
+
+    @BeforeClass
+    public static void beforeTests() {
+        try {
+            seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
+        } catch (FileNotFoundException e) {
+            throw new StingException("unable to load the sequence dictionary");
+        }
+        GenomeLocParser.setupRefContigOrdering(seq);
+
+    }
+
+    public BufferedReader openFile(String filename) {
+        try {
+            return new BufferedReader(new FileReader(filename));
+        } catch (FileNotFoundException e) {
+            throw new StingException("Couldn't open file " + filename);
+        }
+
+    }
+
+    @Test
+    // count the number of SNP's between 10M and 11M on chr1 in dbSNP
+    public void testDBSNPInput() {
+        BufferedReader stream = openFile("/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod");
+        int snpCount = 0;
+        int indelCount = 0;
+        try {
+            String line = stream.readLine();
+            rodDbSNP rod = new rodDbSNP("db");
+            boolean stop = false;
+            while (line != null && !stop) {
+                rod.parseLine(null,line.split("\t"));
+                rodDbSNP var = (rodDbSNP)rod;
+                if (rod.isSNP()) {
+                    // quick check, if we're not triallelic, make sure the ref is right
+                    if (var.getRefSnpFWD() == var.refBases.charAt(0) || var.getAltSnpFWD() == var.refBases.charAt(0))
+                        // also make sure the ref is a single character
+                        if (var.refBases.length() == 1)
+                            Assert.assertTrue(var.refBases.charAt(0)==var.getRefSnpFWD());
+                    if (var.getLocation().getContig().equals("1") &&
+                            var.getLocation().getStart() >= 10000000 &&
+                            var.getLocation().getStart() <= 11000000) {
+                        if (var.isSNP()) {
+                            snpCount++;
+                        }
+                        
+                    }
+                }
+                if (rod.isIndel())
+                    indelCount++;
+
+                stop = (var.getLocation().getContig().equals("1") && var.getLocation().getStart() > 11000000);
+                line = stream.readLine();
+            }
+            Assert.assertEquals(3717,snpCount);
+            Assert.assertEquals(9902,indelCount);
+
+        } catch (IOException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+        }
+    }
+
+
+}
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
index ea0189104..1f44d2a78 100644
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
@@ -19,7 +19,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalVariantROD() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("094c0adb8e4ae4de424f26482fd43152");
+        md5.add("013d13d405f33b0fe4038f5aea087e7f");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -50,7 +50,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalVariantRODConfSix() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("eb8716965fa1df93954c5a22b0aeda7c");
+        md5.add("422d94ab60a3db42b0a5dc9c254b78f4");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -82,7 +82,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
      @Test
     public void testEvalVariantRODOutputViolations() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("9449cfb668f5175013161d2f287c30ff");
+        md5.add("8e613d57fd770ff04eb6531f583f4448");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -114,7 +114,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testEvalGenotypeROD() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("ff2bf8987e288198b28201b5c3121c0e");
+        md5.add("439c2983a6e1250cd845c686a0e5a085");
         /**
          * the above MD5 was calculated after running the following command:
          *