diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
new file mode 100755
index 000000000..abe61d420
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.gatk.walkers.filters;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class VariantFiltrationIntegrationTest extends WalkerTest {
+    @Test
+    public void testIntervals() {
+
+        String[] md5DoC = {"c6ac824171bc2abcd6a896ba07d0c072", "21c8e1f9dc65fdfb39347547f9b04011"};
+        WalkerTestSpec spec1 = new WalkerTestSpec(
+                "-T VariantFiltration -X DepthOfCoverage:max=70 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5DoC));
+        executeTest("testDoCFilter", spec1);
+
+        String[] md5AlleleBalance = {"06fa8901c6823766b89ec28acc435c47", "a13e4ce6260bf9f33ca99dc808b8e6ad"};
+        WalkerTestSpec spec2 = new WalkerTestSpec(
+                "-T VariantFiltration -X AlleleBalance:low=0.25,high=0.75 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5AlleleBalance));
+        executeTest("testAlleleBalanceFilter", spec2);
+
+        String[] md5Strand = {"3f77d329a2f9223423a19665cf7eebbd", "0f7db0aad764268ee8fa3b857df8d87d"};
+        WalkerTestSpec spec3 = new WalkerTestSpec(
+                "-T VariantFiltration -X FisherStrand:pvalue=0.0001 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5Strand));
+        executeTest("testStrandFilter", spec3);
+
+        String[] md5Lod = {"2c4251fc21998705458a9d25386f522f", "7e0c4f2b0fda85fd2891eee76c396a55"};
+        WalkerTestSpec spec4 = new WalkerTestSpec(
+                "-T VariantFiltration -X LodThreshold:lod=10 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5Lod));
+        executeTest("testLodFilter", spec4);
+
+        String[] md5MQ0 = {"8d0dbd951241177dddc4aab8b747ed86", "3203de335621851bccf596242b079e23"};
+        WalkerTestSpec spec5 = new WalkerTestSpec(
+                "-T VariantFiltration -X MappingQualityZero:max=70 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5MQ0));
+        executeTest("testMappingQuality0Filter", spec5);
+
+        String[] md5MQ = {"638719c44704fbac599dfc957a3dce06", "07c5e5b8b3b49a53a6617e63c9e56c71"};
+        WalkerTestSpec spec6 = new WalkerTestSpec(
+                "-T VariantFiltration -X MappingQuality:min=5 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5MQ));
+        executeTest("testRMSMappingQualityFilter", spec6);
+
+        String[] md5OnOff = {"638719c44704fbac599dfc957a3dce06", "07c5e5b8b3b49a53a6617e63c9e56c71"};
+        WalkerTestSpec spec7 = new WalkerTestSpec(
+                "-T VariantFiltration -X OnOffGenotypeRatio:threshold=0.8 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5OnOff));
+        executeTest("testOnOffGenotypeFilter", spec7);
+
+        String[] md5Clusters = {"22d6c46e3971573159d195c8d93e9293", "8fa6b6ffc93ee7fb8d6b52a7fb7815ef"};
+        WalkerTestSpec spec8 = new WalkerTestSpec(
+                "-T VariantFiltration -X ClusteredSnps:window=10,snps=3 -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5Clusters));
+        executeTest("testClusteredSnpsFilter", spec8);
+
+        String[] md5Indels = {"3d9ebd5ada1c355e44245a64bc801b11", "8e0e915a1cb63d7049e0671ed00101fe"};
+        WalkerTestSpec spec9 = new WalkerTestSpec(
+                "-T VariantFiltration -X IndelArtifact -B indels,PointIndel,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.indels -B cleaned,CleanedOutSNP,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.realigner_badsnps -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 -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
+                 2,
+                 Arrays.asList(md5Indels));
+        executeTest("testIndelArtifactFilter", spec9);
+
+
+
+
+
+
+    }
+}
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