diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java
new file mode 100755
index 000000000..7a3585b52
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java
@@ -0,0 +1,94 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.junit.Test;
+import org.junit.Assert;
+import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.BasicGenotype;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.playground.gatk.walkers.varianteval.ConcordanceTruthTable;
+import org.broadinstitute.sting.BaseTest;
+
+import java.util.List;
+import java.util.ArrayList;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: Nov 19, 2009
+ * Time: 9:40:51 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ConcordanceTruthTableTest extends BaseTest {
+
+    @Test
+    public void testAlleleFrequencyCalculation() {
+
+        ConcordanceTruthTable ctt = new ConcordanceTruthTable(3);
+        // this will test the count of non-reference alleles at a T/G polymorphic site
+        Genotype ref1 = new BasicGenotype(null,"GG",'G',30);
+        Genotype ref2 = new BasicGenotype(null,"GG",'G',30);
+        Genotype ref3 = new BasicGenotype(null,"GG",'G',30);
+        Genotype het1 = new BasicGenotype(null,"GT",'G',32);
+        Genotype het2 = new BasicGenotype(null,"GT",'G',28);
+        Genotype hom1 = new BasicGenotype(null,"TT",'G',40);
+        Genotype hom2 = new BasicGenotype(null,"TT",'G',27);
+
+        List<Pair<Genotype,Genotype>> oneHom = new ArrayList<Pair<Genotype,Genotype>>(4);
+        oneHom.add(new Pair<Genotype,Genotype>(ref1,null));
+        oneHom.add(new Pair<Genotype,Genotype>(ref2,null));
+        oneHom.add(new Pair<Genotype,Genotype>(ref3,null));
+        oneHom.add(new Pair<Genotype,Genotype>(hom2,null));
+
+        List<Pair<Genotype,Genotype>> oneHet = new ArrayList<Pair<Genotype,Genotype>>(4);
+        oneHet.add(new Pair<Genotype,Genotype>(ref1,null));
+        oneHet.add(new Pair<Genotype,Genotype>(ref2,null));
+        oneHet.add(new Pair<Genotype,Genotype>(ref3,null));
+        oneHet.add(new Pair<Genotype,Genotype>(het1,null));
+
+        List<Pair<Genotype,Genotype>> twoHetOneHom = new ArrayList<Pair<Genotype,Genotype>>(5);
+        twoHetOneHom.add(new Pair<Genotype,Genotype>(ref1,null));
+        twoHetOneHom.add(new Pair<Genotype,Genotype>(ref2,null));
+        twoHetOneHom.add(new Pair<Genotype,Genotype>(ref3,null));
+        twoHetOneHom.add(new Pair<Genotype,Genotype>(het1,null));
+        twoHetOneHom.add(new Pair<Genotype,Genotype>(het2,null));
+        twoHetOneHom.add(new Pair<Genotype,Genotype>(hom1,null));
+
+        List<Pair<Genotype,Genotype>> twoHetTwoHom = new ArrayList<Pair<Genotype,Genotype>>(7);
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(ref1,null));
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(ref2,null));
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(ref3,null));
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(het1,null));
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(het2,null));
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(hom1,null));
+        twoHetTwoHom.add(new Pair<Genotype,Genotype>(hom2,null));
+
+        List<Pair<Genotype,Genotype>> hetHomNoRef = new ArrayList<Pair<Genotype,Genotype>>(2);
+        hetHomNoRef.add(new Pair<Genotype,Genotype>(het2,null));
+        hetHomNoRef.add(new Pair<Genotype,Genotype>(hom2,null));
+
+        List<Pair<Genotype,Genotype>> homNoRef = new ArrayList<Pair<Genotype,Genotype>>(1);
+        homNoRef.add(new Pair<Genotype,Genotype>(hom1,null));
+
+        Pair<Genotype,Integer> countShouldBeOne = ctt.getPooledAlleleFrequency(oneHet,'G');
+        Pair<Genotype,Integer> countShouldBeTwo = ctt.getPooledAlleleFrequency(oneHom,'G');
+        Pair<Genotype,Integer> countShouldBeFour = ctt.getPooledAlleleFrequency(twoHetOneHom,'G');
+        Pair<Genotype,Integer> countShouldBeSix = ctt.getPooledAlleleFrequency(twoHetTwoHom,'G');
+        Pair<Genotype,Integer> countShouldBeThree = ctt.getPooledAlleleFrequency(hetHomNoRef,'G');
+        Pair<Genotype,Integer> countShouldBeTwoHereToo = ctt.getPooledAlleleFrequency(homNoRef, 'G');
+
+
+        logger.warn("Testing single het");
+        Assert.assertTrue(countShouldBeOne.getSecond() == 1);
+        logger.warn("Testing single hom");
+        Assert.assertTrue(countShouldBeTwo.getSecond() == 2);
+        logger.warn("Testing two hets + hom");
+        Assert.assertTrue(countShouldBeFour.getSecond() == 4);
+        logger.warn("Testing two hets + two homs");
+        Assert.assertTrue(countShouldBeSix.getSecond() == 6);
+        logger.warn("Testing het + hom without ref");
+        Assert.assertTrue(countShouldBeThree.getSecond() == 3);
+        logger.warn("Testing hom without ref");
+        Assert.assertTrue(countShouldBeTwoHereToo.getSecond() == 2);
+    }
+}