Took latest VEIT and updated to use dbsnp132 vcf
This commit is contained in:
Mark DePristo
parent
0ef85647f7
commit
41b3840d26
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@ -4,8 +4,6 @@ import org.broadinstitute.sting.WalkerTest;
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import org.testng.annotations.Test;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.Map;
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public class VariantEvalIntegrationTest extends WalkerTest {
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private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval";
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@ -16,27 +14,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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private static String cmdRoot = "-T VariantEval" +
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" -R " + b36KGReference;
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private static String root = cmdRoot +
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" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
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" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
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" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
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private static String rootGZ = cmdRoot +
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" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
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" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
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" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
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// TODO -- I can't seem to reindex this VCF using Tabix without it causing failures. Looking into it. [EB]
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// private static String[] testsEnumerations = {root, rootGZ};
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private static String[] testsEnumerations = {root};
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@Test
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public void testFundamentalsCountVariantsSNPsAndIndels() {
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WalkerTestSpec spec = new WalkerTestSpec(
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -45,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("48b8417c1f8bd74ff7b9808580abd2a2")
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Arrays.asList("bced1842c78fbabb089dd12b7087050d")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
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}
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@ -56,7 +40,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -66,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("86d45ecefdf5849c55b3ca8f82a3d525")
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Arrays.asList("06510bd37ffaa39e817ca0dcaf8f8ac2")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
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}
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@ -77,7 +61,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -88,7 +72,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("3d18901ec1766aa2e748eac913f5ddcd")
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Arrays.asList("19c5b1b6396921c5b1059a2849ae4fcc")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
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}
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@ -99,7 +83,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -109,7 +93,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("677fe398643e62a10d6739d36a720a12")
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Arrays.asList("a71f8d81cf166cd97ac628092650964a")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
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}
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@ -120,7 +104,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -130,7 +114,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("5fb44fd7cb00941c986a9941e43e44cd")
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Arrays.asList("4dabe0658232f6174188515db6dfe112")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
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}
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@ -141,7 +125,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -151,7 +135,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("daaca7ef3b7313e5af217cbc6f37c9e2")
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Arrays.asList("3340587f10ceff83e5567ddfd1a9a60e")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
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}
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@ -162,7 +146,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -172,7 +156,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("97c466f8ffd0fcf2c30ef08669d213d9")
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Arrays.asList("c730c7ee31c8138cef6efd8dd04fbbfc")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
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}
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@ -183,7 +167,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -195,7 +179,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("df8cdfcf3d0c2fc795812c6eae6a76f8")
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Arrays.asList("2559ca8f454b03e81561f6947f79df18")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
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}
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@ -206,7 +190,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestVCF,
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"-noEV",
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"-EV CountVariants",
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@ -220,7 +204,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("c7aed12265e2b2311d17a0cc8a29f6aa")
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Arrays.asList("23aa5f97641d2fd033095f21c51d2f37")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
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}
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@ -239,7 +223,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("d44c8f44384189a09eea85a8e89d7299")
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Arrays.asList("a69dd3f06903b3f374c6d6f010c653e0")
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);
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executeTest("testFundamentalsCountVariantsNoCompRod", spec);
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}
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@ -247,11 +231,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testSelect1() {
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String extraArgs = "-L 1:1-10,000,000";
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for (String tests : testsEnumerations) {
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WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
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1, Arrays.asList("96860dedea0fa6b46c07f46b847fea42"));
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executeTestParallel("testSelect1", spec);
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}
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String tests = cmdRoot +
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" -B:dbsnp,VCF " + b36dbSNP129 +
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" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
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" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
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1, Arrays.asList("db95c8af8ba549d38ca6741a59fd6892"));
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executeTestParallel("testSelect1", spec);
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}
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@Test
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@ -260,14 +246,14 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
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1,
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Arrays.asList("e4c981f7f5d78680c71310fc9be9a1c1"));
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Arrays.asList("96f27163f16bb945f19c6623cd6db34e"));
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executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
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}
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@Test
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public void testCompVsEvalAC() {
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String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("162daa5039e1965eb2423a8589339a69"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
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executeTestParallel("testCompVsEvalAC",spec);
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}
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@ -278,14 +264,14 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testTranches() {
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String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("90cd98044e754b80034a9f4e6d2c55b9"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("984df6e94a546294fc7e0846cbac2dfe"));
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executeTestParallel("testTranches",spec);
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}
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@Test
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public void testCompOverlap() {
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String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("70aa420929de7f888a6f48c2d01bbcda"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("462d4784dd55294ef9d5118217b157a5"));
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executeTestParallel("testCompOverlap",spec);
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}
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@ -294,10 +280,10 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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String extraArgs = "-T VariantEval -R " +
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b37KGReference +
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" -L 20" +
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" -B:dbsnp,vcf " + b37dbSNP132 +
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" -B:dbsnp,VCF " + b37dbSNP132 +
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" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
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" -noST -ST Novelty -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("58fdc6c42fade3007537bb99fb3ce738"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("61c36fb6cc75172e2b22a44edeae85e0"));
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executeTestParallel("testEvalTrackWithoutGenotypes",spec);
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}
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@ -305,11 +291,11 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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public void testMultipleEvalTracksWithoutGenotypes() {
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String extraArgs = "-T VariantEval -R " + b37KGReference +
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" -L 20" +
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" -B:dbsnp,vcf " + b37dbSNP132 +
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" -B:dbsnp,VCF " + b37dbSNP132 +
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" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
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" -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
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" -noST -ST Novelty -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("34df2815d27e5e62f1694731a7e7953c"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("79089484097614b7ab81bbc3ad3a892a"));
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executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
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}
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@ -326,19 +312,19 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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" -noST -noEV -ST Novelty -EV CompOverlap" +
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" -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("20332902ae36a84b2fd80405410815f1"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9f906c04a4553d649b51ae67e0a25113"));
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executeTestParallel("testMultipleCompTracks",spec);
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}
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@Test
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public void testPerSampleAndSubsettedSampleHaveSameResults() {
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String md5 = "9d61f6e2c8592dcf616712a2c587b2af";
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String md5 = "97a16a99a43d2384cfabc39d36647419";
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WalkerTestSpec spec = new WalkerTestSpec(
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestSNPsVCF,
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"-noEV",
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"-EV CompOverlap",
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@ -356,7 +342,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
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"-noEV",
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"-EV CompOverlap",
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@ -377,7 +363,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
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"-B:dbsnp,VCF " + b37dbSNP132,
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"-B:eval,VCF " + fundamentalTestSNPsVCF,
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"-noEV",
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"-EV CountVariants",
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@ -387,7 +373,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("bf324e4c87fe0d21170fcd2a67a20371")
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Arrays.asList("44464fe7c89a56cf128a932ef640f7da")
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);
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executeTest("testAlleleCountStrat", spec);
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}
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