SB tables should be created even if the ref or alt columns have no counts. This is so that FS/SOR will still be calculated when the variant is extremely high or low frequency.
-- Removed long running HC integration test... sorry
This commit is contained in:
Ryan Poplin
parent
5c45641051
commit
e14bff212d
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@ -93,8 +93,8 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation {
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* @return true if it passes the minimum threshold, false otherwise
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*/
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protected static boolean passesMinimumThreshold(final int[] data, final int minCount) {
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// the ref and alt totals must each be greater than MIN_COUNT
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return data[0] + data[1] > minCount && data[2] + data[3] > minCount;
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// the ref and alt totals must be greater than MIN_COUNT
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return data[0] + data[1] + data[2] + data[3] > minCount;
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}
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/**
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@ -89,7 +89,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("ff21ad7bb0d6bcabcee6b95d975570fc"));
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Arrays.asList("7531245db11cc0bb4ddaea18e109e2b8"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -97,7 +97,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("cb463a56d0b5bc66940f844e56265c14"));
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Arrays.asList("213560f395280e6a066d0b0497ce8881"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -123,7 +123,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("d57ca04b4ceb2f25b31bc0cbd88bca6b"));
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Arrays.asList("73b2f3608c778c1b001833245f49ede8"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -131,7 +131,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("9cc0cf19070d951b1979e069552810f1"));
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Arrays.asList("d8089c5874ff35a7fd7e35ebd7d3b137"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -69,16 +69,16 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
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@Test(enabled = true)
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public void testBOTH_GGA_Pools() {
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "c2932cc77611f13cc8a14e87d055a8f8");
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "05b8af0db7b009721df209eea96bdf1a");
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}
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@Test(enabled = true)
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public void testINDEL_GGA_Pools() {
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "a0648992f049ed59fab0ef753d2d0c03");
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executor.PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "1ac510860b295d66e1da7b27ba7cafb8");
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}
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "fcfe18bd4c6087b21959d3c31ec177da");
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "ae90d6be28c19e455083a47bc95c3b1b");
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}
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}
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@ -58,16 +58,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","ef7a6ee4ec7e20e5ce28fc50d3362d3d");
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9fc4f04105bde31bafc93548745cb67e");
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}
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@Test(enabled = true)
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public void testMT_SNP_DISCOVERY_sp4() {
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executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","fc75733fcdd8079e7f7743961a1f36be");
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executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","f5bd19784f482efe7254b04209224dca");
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}
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@Test(enabled = true)
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public void testMT_SNP_GGA_sp10() {
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executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "86cdfc291f995036658bfc10773db107");
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executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "654059dda19cb2cf546097e44753ea14");
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}
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}
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@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("bb8c1b2e9343c79133d8efb51ec2192e"));
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Arrays.asList("8a4de9e1f59cffe80a4372cf02fe809e"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -100,7 +100,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("f5e5148cac1526136f9f2559fe3b49fa"));
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Arrays.asList("2b92df91a9337b9d9f03db5699bb41f2"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -110,7 +110,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("209db887bfe1aac8bd62544aa8afa2b5"));
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Arrays.asList("591c9a7bd7d64974b4a2dd932fdef138"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
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}
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@ -120,7 +120,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
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+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("83b32ea956809654590abd5e0c029d4d"));
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Arrays.asList("e784b6d1b3725f72a2c42b19e8d24cb1"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
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}
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@ -135,7 +135,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
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"low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
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Arrays.asList("25815c1968450ddd009b983d65809c50"));
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Arrays.asList("5cec2cf712abf11662081471a911ab1f"));
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executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
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}
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@ -176,7 +176,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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public void testMinIndelFraction0() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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assessMinIndelFraction + " -minIndelFrac 0.0", 1,
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Arrays.asList("0d9a3129f680c4a4f41b08154fd836a4"));
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Arrays.asList("96c2ab043f523c7676e4bc36dd3c9d0b"));
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executeTest("test minIndelFraction 0.0", spec);
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}
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@ -184,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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public void testMinIndelFraction25() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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assessMinIndelFraction + " -minIndelFrac 0.25", 1,
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Arrays.asList("e910304c25a277b63d8fa8167d4a8b88"));
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Arrays.asList("53ce3aa9ee16302ab2ec21f742b5e157"));
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executeTest("test minIndelFraction 0.25", spec);
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}
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@ -151,7 +151,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testNoPrior() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.33333 -inputPrior 0.33333", 1,
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Arrays.asList("9ee4f1ee1827a6726bfac1220a6a7c40"));
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Arrays.asList("7ac60bdc355d97c0939e644b58de47d7"));
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executeTest("test no prior 1", spec1);
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}
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@ -169,7 +169,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void emitPLsAtAllSites() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
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Arrays.asList("85dee5da72c4154e130527c4e6329c07"));
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Arrays.asList("552aced1b1ef7e4a554223f4719f9560"));
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// GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
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spec1.disableShadowBCF();
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@ -64,7 +64,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMultiSamplePilot1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("03ff28802a2e06e0a623d9a5df66d237"));
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Arrays.asList("058b54cff14527485c7b1ab035ebb6c4"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -72,7 +72,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testWithAllelesPassedIn1() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("85d0e5c086dc642d55124f0e88e7326b"));
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Arrays.asList("ebfcc3dd8c1788929cb50050c5d456df"));
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executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
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}
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@ -80,7 +80,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testWithAllelesPassedIn2() {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("11783a280df9bf621840c300edd0401a"));
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Arrays.asList("3e646003c5b93da80c7d8e5d0ff2ee4e"));
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executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
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}
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@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMultipleSNPAlleles() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
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Arrays.asList("eac8b071bd2fa89889d51de8be84624a"));
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Arrays.asList("c13b5cfd5e0dc47d9709b9e9a948b1e7"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -112,7 +112,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
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Arrays.asList("7f912aa5166f6ed16166daac1e5c0935"));
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Arrays.asList("bc5a143868e3ad3acc9bb7c09798cdf2"));
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executeTest("test reverse trim", spec);
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}
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@ -120,7 +120,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMismatchedPLs() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
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Arrays.asList("ab22f70f5c65d45f9754e7064e5a152c"));
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Arrays.asList("822981d2707cb78475bc1b4a5b23f889"));
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executeTest("test mismatched PLs", spec);
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}
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}
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleComplex1() {
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "bb761c6cd0893e7e96c56bf1d8494588");
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "c2a6bd61aee2edab2439eeb14bdc1aeb");
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}
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private void HCTestSymbolicVariants(String bam, String args, String md5) {
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@ -88,13 +88,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleGGAComplex() {
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HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
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"fb1042487efb03896f482c08d7eb2671");
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"f23ac8256edfdf949cefcb245c227abb");
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}
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@Test
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public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
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HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
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"9a6e314d7a8fe1c4a9ff5048544cb670");
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"fb9f244c09ac6781e2a984e90e0cd340");
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}
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private void HCTestComplexConsensusMode(String bam, String args, String md5) {
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@ -106,7 +106,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
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HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
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"1e4af2f8fc97e0b07e625f142374742f");
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"23dab7ca085f13b3b23954a94630d04d");
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}
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}
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@ -67,9 +67,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
|
||||
|
||||
// this functionality can be adapted to provide input data for whatever you might want in your data
|
||||
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "080cf92bfcb7db4273e2d723045daee5"});
|
||||
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "a4c0a28a451069faaac937e45c701043"});
|
||||
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0bc25b42dc73eeadb23a35227684172c"});
|
||||
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "97cfa815579021d84b17ead791b66af2"});
|
||||
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "55638f5886e4a66d9787e31ac65481c7"});
|
||||
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "9ea9d65ad7fc0c9ed7880746d5e6ce7f"});
|
||||
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "c95a777e3aac50b9f29302919a00ba4e"});
|
||||
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "05860d40923e8b074576c787037c5768"});
|
||||
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "f3abc3050b2708fc78c903fb70ac253e"});
|
||||
|
|
@ -149,7 +149,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
public void testNoCallGVCFMissingPLsBugFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7c263d77bf831551366c6e36233b46ce"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("8e6972866400eae202e72c959a8333a3"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -84,7 +84,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSample() {
|
||||
HCTest(CEUTRIO_BAM, "", "030b45c91879eb41f30abbd10ed88fa9");
|
||||
HCTest(CEUTRIO_BAM, "", "7c4b9454f80f28386cd1ca6634b3db42");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -104,7 +104,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerGraphBasedMultiSample() {
|
||||
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "d530933588810bb4cf04a9783d187433");
|
||||
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "4d7a929ca7e15ec3e0173e4a4381a704");
|
||||
}
|
||||
|
||||
@Test(enabled = false) // can't annotate the rsID's yet
|
||||
|
|
@ -115,7 +115,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGA() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"844d1daa4a8835f4c7e10d0d8bbfe510");
|
||||
"5d824bf8a95f21fbb6de99d180f72a21");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -227,7 +227,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestDBSNPAnnotationWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
Arrays.asList("d357f6fe3f1350f886b0df5a207e9f6f"));
|
||||
Arrays.asList("5537548b7d0c5615242695c48b4e8ecd"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -244,7 +244,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestDBSNPAnnotationWGSGraphBased() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
Arrays.asList("4e43cf47d32210ee6a6880af3bbfcc52"));
|
||||
Arrays.asList("b25cbde7d1ad7efc43b894445f349a9f"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -276,7 +276,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestAggressivePcrIndelModelWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
|
||||
Arrays.asList("9297d4f5a9eaab253bea1ec19a8581c2"));
|
||||
Arrays.asList("91606273478c01613016e00f0f39ec8c"));
|
||||
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -284,7 +284,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestConservativePcrIndelModelWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
|
||||
Arrays.asList("de2b002e0311c8fac7d053ecf8cb41f8"));
|
||||
Arrays.asList("f52490340b7ced98700f93e09bec05f3"));
|
||||
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -304,7 +304,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
|
||||
b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list",
|
||||
HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5c1323d441ab083dbb569831959a9250"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("8328a0f44eb8aa3b891ace2207ed488e"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
|
||||
}
|
||||
|
|
@ -318,16 +318,6 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBadLikelihoodsDueToBadHaplotypeSelectionFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header ",
|
||||
hg19RefereneWithChrPrefixInChromosomeNames, privateTestDir + "bad-likelihoods.bam", privateTestDir + "bad-likelihoods.interval_list",
|
||||
HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e36179dcdfb6f2a4269d08543479e97c"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testBadLikelihoodsDueToBadHaplotypeSelectionFix", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix() {
|
||||
final String SHORT_INTERVAL = "12:7342264-7342464";
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-20,000,000", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("51bf72a5eb3b2592d319072e4ce26c92"));
|
||||
Arrays.asList("e61d4cbfd21f102c2e6c0bd56cb68312"));
|
||||
executeTest("combineSingleSamplePipelineGVCF", spec);
|
||||
}
|
||||
|
||||
|
|
@ -94,7 +94,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-20,000,000", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("46044467b366db1c15a48a429b7c2291"));
|
||||
Arrays.asList("1c553decc3f9fe1d752137a7f34d7e4e"));
|
||||
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
|
||||
}
|
||||
|
||||
|
|
@ -106,7 +106,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
|
||||
1,
|
||||
Arrays.asList("52655b4a693bc79e1029e47276a2653b"));
|
||||
Arrays.asList("e6952f19e692091332809c59069a1eab"));
|
||||
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
|
||||
}
|
||||
|
||||
|
|
@ -116,7 +116,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
|
||||
" -V " + privateTestDir + "gvcfExample1.vcf",
|
||||
1,
|
||||
Arrays.asList("6fe339b17f4e5621e849d842c64a6e42"));
|
||||
Arrays.asList("b18ddcf828227c07f1b38d99c91f6e09"));
|
||||
executeTest("testJustOneSample", spec);
|
||||
}
|
||||
|
||||
|
|
@ -127,7 +127,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V " + privateTestDir + "gvcfExample1.vcf" +
|
||||
" -V " + privateTestDir + "gvcfExample2.vcf",
|
||||
1,
|
||||
Arrays.asList("aad7bda0f3c60689b61e87d641b62856"));
|
||||
Arrays.asList("a453f2e15b20f8cf0edadb998cb883d5"));
|
||||
executeTest("testSamplesWithDifferentLs", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue