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Adding indel vqsr integration test

This commit is contained in:
Ryan Poplin 2011-09-08 10:38:13 -04:00
parent 9cba1019c8
commit 2636d216de
1 changed files with 48 additions and 0 deletions
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48
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -73,5 +73,53 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
Arrays.asList(params.cutVCFMD5));
executeTest("testApplyRecalibration-"+params.inVCF, spec);
}
VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
"6d7ee4cb651c8b666e4a4523363caaff", // tranches
"4759b111a5aa53975d46e0f22c7983bf", // recal file
"5d7e07d8813db96ba3f3dfe4737f83d1"); // cut VCF
@DataProvider(name = "VRIndelTest")
public Object[][] createData2() {
return new Object[][]{ {indel} };
}
@Test(dataProvider = "VRIndelTest")
public void testVariantRecalibratorIndel(VRTest params) {
//System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -known:prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -training:prior=15.0 " + comparisonDataLocation + "Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf" +
" -truth:prior=15.0 " + comparisonDataLocation + "Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf" +
" -T VariantRecalibrator" +
" -input " + params.inVCF +
" -L 20:1,000,000-40,000,000" +
" -an QD -an ReadPosRankSum -an HaplotypeScore" +
" -percentBad 0.08" +
" -mode INDEL -mG 3" +
" --minNumBadVariants 0" +
" --trustAllPolymorphic" + // for speed
" -recalFile %s" +
" -tranchesFile %s",
Arrays.asList(params.recalMD5, params.tranchesMD5));
executeTest("testVariantRecalibratorIndel-"+params.inVCF, spec).getFirst();
}
@Test(dataProvider = "VRIndelTest",dependsOnMethods="testVariantRecalibratorIndel")
public void testApplyRecalibrationIndel(VRTest params) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -T ApplyRecalibration" +
" -L 20:12,000,000-30,000,000" +
" -mode INDEL" +
" -NO_HEADER" +
" -input " + params.inVCF +
" -o %s" +
" -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) +
" -recalFile " + MD5DB.getMD5FilePath(params.recalMD5, null),
Arrays.asList(params.cutVCFMD5));
executeTest("testApplyRecalibrationIndel-"+params.inVCF, spec);
}
}