diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperIntegrationTest.java
deleted file mode 100755
index d83349d66..000000000
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperIntegrationTest.java
+++ /dev/null
@@ -1,190 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.genotyper;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.junit.Test;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-
-public class SingleSampleGenotyperIntegrationTest extends WalkerTest {
-    public static String baseTestString() {
-        return "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s";
-    }
-
-    public static String testGeliLod5() {
-        return baseTestString() + " --variant_output_format GELI -lod 5";
-    }
-
-    private static String OneMb1StateMD5 = "cba4436066b5d88a461cc3eba74ad944";
-    private static String OneMb3StateMD5 = "799dde914dd4afbffca9502b7f284780";
-    private static String OneMbEmpiricalMD5 = "2b99b3c667c8ac94e8268b17e6979073";
-
-//    private static String oneMbMD5(BaseMismatchModel m) {
-//        switch (m) {
-//            case ONE_STATE: return OneMb1StateMD5;
-//            case THREE_STATE: return OneMb3StateMD5;
-//            case EMPIRICAL: return OneMbEmpiricalMD5;
-//            default: throw new RuntimeException("Unexpected BaseMismatchModel " + m);
-//        }
-//    }
-
-    // Uncomment to not check outputs against expectations
-    //protected boolean parameterize() {
-    //    return true;
-    //}
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing calls with SLX, 454, and SOLID data
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    @Test
-    public void testMultiTechnologies() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper" +
-                        " -R /broad/1KG/reference/human_b36_both.fasta" +
-                        " -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
-                        " -varout %s" +
-                        " -L 1:10,000,000-10,100,000" +
-                        " -bm empirical",
-                1,
-                Arrays.asList("0a923f676111b9bc27ccb1a9b97eafcc"));
-
-        executeTest(String.format("testMultiTechnologies"), spec);
-    }    
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing the cache
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    /*
-    @Test
-    public void testCache() {
-        for ( BaseMismatchModel model : BaseMismatchModel.values() ) {
-            // calculated the expected value without the cache enabled
-            WalkerTest.WalkerTestSpec withoutCacheSpec = new WalkerTest.WalkerTestSpec(
-                    testGeliLod5() + " -L 1:10,000,000-10,100,000 --disableCache -m " + model.toString(), 1,
-                    Arrays.asList(""));
-            List<String> withoutCache = executeTest("empirical1MbTest", withoutCacheSpec ).getSecond();
-
-            WalkerTest.WalkerTestSpec withCacheSpec = new WalkerTest.WalkerTestSpec(
-                    testGeliLod5() + " -L 1:10,000,000-10,100,000 -bm " + model.toString(), 1,
-                    withoutCache);
-            executeTest(String.format("testCache[%s]", model), withCacheSpec );
-        }
-    }
-    */
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing genotype mode
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    @Test
-    public void genotypeTest() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                testGeliLod5() + " -L 1:10,000,000-10,100,000 -bm empirical --genotype", 1,
-                Arrays.asList("436c0e3365f61bf1d06eb630c025e51b"));
-        executeTest("genotypeTest", spec);
-    }
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // basic base calling models
-    //
-    // --------------------------------------------------------------------------------------------------------------
-
-    @Test
-    public void oneState100bpTest() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( testGeliLod5() + " -L 1:10,000,000-10,000,100 -bm one_state", 1, Arrays.asList("3cd402d889c015be4a318123468f4262"));
-        executeTest("oneState100bpTest", spec);
-    }
-
-    @Test
-    public void oneState1MbTest() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm one_state",
-                1, Arrays.asList(OneMb1StateMD5));
-        executeTest("oneState1MbTest", spec);
-    }
-
-    @Test
-    public void threeState1MbTest() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm three_state", 1,
-                Arrays.asList(OneMb3StateMD5));
-        executeTest("threeState1MbTest", spec);
-    }
-
-    @Test
-    public void empirical1MbTest() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm empirical", 1,
-                Arrays.asList(OneMbEmpiricalMD5));
-        executeTest("empirical1MbTest", spec);
-    }
-
-
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing output formats
-    //
-    // --------------------------------------------------------------------------------------------------------------
-
-    //@Argument(fullName = "variant_output_format", shortName = "vf", doc = "File format to be used", required = false)
-    //public GenotypeWriterFactory.GENOTYPE_FORMAT VAR_FORMAT = GenotypeWriterFactory.GENOTYPE_FORMAT.GELI;
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing LOD thresholding
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    @Test
-    public void testLOD() {
-        HashMap<Double, String> e = new HashMap<Double, String>();
-        e.put( 10.0, "3ec7815482112e0b9b4487ec69a52b67" );
-        e.put( 3.0, "20da42fdce2e1c97d9c8d4935d31125d" );
-
-        for ( Map.Entry<Double, String> entry : e.entrySet() ) {
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    baseTestString() + " --variant_output_format GELI -L 1:10,000,000-11,000,000 -bm EMPIRICAL -lod " + entry.getKey(), 1,
-                    Arrays.asList(entry.getValue()));
-            executeTest("testLOD", spec);
-        }
-    }
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing hetero setting
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    @Test
-    public void testHeterozyosity() {
-        HashMap<Double, String> e = new HashMap<Double, String>();
-        e.put( 0.01, "e7494e6a62bd91ca02537c327a104395" );
-        e.put( 0.0001, "1d51c711353d0db5b54dd0d2a7899c49" );
-        e.put( 1.0 / 1850, "873f558a2c07ec40635e35d275b12d69" );
-
-        for ( Map.Entry<Double, String> entry : e.entrySet() ) {
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    testGeliLod5() + " -L 1:10,000,000-11,000,000 -bm EMPIRICAL --heterozygosity " + entry.getKey(), 1,
-                    Arrays.asList(entry.getValue()));
-            executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec);
-        }
-    }
-
-    /**
-     * test the output of a binary geli file
-      */
-    @Test
-    public void empirical1MbTestBinaryGeli() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseTestString() + " -L 1:10,000,000-11,000,000 -m empirical --variant_output_format GELI_BINARY -lod 5", 1,
-                Arrays.asList("17e9fc04b2a05cafc53562997c28e127"));
-        executeTest("empirical1MbTest", spec);
-    }
-
-}