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Change the truth VCF

This commit is contained in:
Ron Levine 2016-11-15 14:56:15 -05:00
parent aac5f55bbe
commit d61b4c7e91
1 changed files with 15 additions and 12 deletions
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27
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -64,6 +64,9 @@ import java.util.Arrays;
import java.util.List;
public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
private static String TRAINING_VCF = comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf";
private static String TRUTH_VCF = comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_genotypes_2141_samples.b37.vcf";
private static class VRTest {
String inVCF;
String aggregateVCF;
@ -93,15 +96,15 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
}
VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
"41e2d951a17de433fe378bb3d9ec75d4", // tranches
"3fe87e69c6a613addb7eff5449e86aa1", // recal file
"78b8f1934d77341df2f6a9fdbd30fa74"); // cut VCF
"3ccb3aa81aebee74d32641105a64ea32", // tranches
"1a87e9cdc66c53891eab61ab39ff2434", // recal file
"217ee1523b6ddaf31f0eb0464b89bab6"); // cut VCF
VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf",
"ce4bfc6619147fe7ce1f8331bbeb86ce", // tranches
"5a298554e9175961f63506c4e42ea78b", // recal file
"f284c0cbb00407cc5273c6f1a871513e"); // cut VCF
"be89401e09dd06817c43f152c789f854", // tranches
"8ce11e7555cccb3f13ea34a9074aec00", // recal file
"c09c2425744e8d914d69a2585dba0e97"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
@ -119,8 +122,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -resource:known=true,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -resource:truth=true,training=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -resource:training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -resource:truth=true,training=true,prior=15.0 " + TRAINING_VCF +
" -resource:training=true,truth=true,prior=12.0 " + TRUTH_VCF +
" -T VariantRecalibrator" +
" -input " + params.inVCF +
" -L 20:1,000,000-40,000,000" +
@ -159,8 +162,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -resource:known=true,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -resource:truth=true,training=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -resource:training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -resource:truth=true,training=true,prior=15.0 " + TRAINING_VCF +
" -resource:training=true,truth=true,prior=12.0 " + TRUTH_VCF +
" -T VariantRecalibrator" +
" -input " + params.inVCF +
" -aggregate " + params.aggregateVCF +
@ -210,8 +213,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b37KGReference +
" -resource:known=true,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" +
" -resource:truth=true,training=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" +
" -resource:training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" +
" -resource:truth=true,training=true,prior=15.0 " + TRAINING_VCF +
" -resource:training=true,truth=true,prior=12.0 " + TRUTH_VCF +
" -T VariantRecalibrator" +
" -input " + params.inVCF +
" -L 20:10,000,000-20,000,000" +