diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java
new file mode 100644
index 000000000..b935ae76b
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCFIntegrationTest.java
@@ -0,0 +1,26 @@
+package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class PlinkToVCFIntegrationTest extends WalkerTest {
+    @Test
+    public void testSNPs() {
+        String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
+        String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PlinkToVCF -B input,Plink,"+testPedFile+" -vcf %s";
+        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
+                Arrays.asList("02dcb683db503599efed0b76daa8fcba"));
+        executeTest("Test SNPs", spec);
+    }
+
+    @Test
+    public void testIndels() {
+        String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
+        String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PlinkToVCF -B input,Plink,"+testPedFile+" -vcf %s";
+        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
+                Arrays.asList("e72c0ab95b279a4d39cc14d40770a801"));
+        executeTest("Test Indels", spec);
+    }
+}
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java
deleted file mode 100644
index d0a5af87f..000000000
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/SequenomToVCFIntegrationTest.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.junit.Test;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: Jan 11, 2010
- * Time: 11:30:59 AM
- * To change this template use File | Settings | File Templates.
- */
-public class SequenomToVCFIntegrationTest extends WalkerTest {
-    //@Test
-    public void testSequenomToVCFWithoutSmartHardy() {
-        String testMD5 = "a16ce402ce4492c8c0552073c0a8bdf5";
-        String testPedFile = "/humgen/gsa-hpprojects/GATK/data/Validation_Data/Sequenom_Test_File.txt";
-        String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -L 1:1000000-2000000 "+
-                          "-T PlinkToVCF -b36contig -ns 10 -B input,Plink,"+testPedFile+" -vcf %s";
-        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs,1, Arrays.asList(testMD5));
-        List<File> result = executeTest("TestSequenomToVCFNoSmartHardy",spec).getFirst();
-    }
-}