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Unfortunately dangling tail recovery is dangerous in exome data. Turning it off by default for now. 

-- disabling HC+VA integration test because, as noted in the comments, it keeps switching PairHMM implementations and giving different results at a particular site used in that particular test
This commit is contained in:
Ryan Poplin 2014-05-22 10:20:01 -04:00
parent cfde6e72bf
commit ec7c4ea2ba
5 changed files with 24 additions and 24 deletions
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6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -285,8 +285,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
protected boolean recoverDanglingHeads = false;
@Hidden
@Argument(fullName="dontRecoverDanglingTails", shortName="dontRecoverDanglingTails", doc="Should we disable dangling tail recovery in the read threading assembler?", required = false)
protected boolean dontRecoverDanglingTails = false;
@Argument(fullName="recoverDanglingTails", shortName="recoverDanglingTails", doc="Should we enable dangling tail recovery in the read threading assembler?", required = false)
protected boolean recoverDanglingTails = false;
@Advanced
@Argument(fullName="consensus", shortName="consensus", doc="In 1000G consensus mode. Inject all provided alleles to the assembly graph but don't forcibly genotype all of them.", required = false)
@ -620,7 +620,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
assemblyEngine.setDebug(SCAC.DEBUG);
assemblyEngine.setDebugGraphTransformations(debugGraphTransformations);
assemblyEngine.setAllowCyclesInKmerGraphToGeneratePaths(allowCyclesInKmerGraphToGeneratePaths);
assemblyEngine.setRecoverDanglingTails(!dontRecoverDanglingTails);
assemblyEngine.setRecoverDanglingTails(recoverDanglingTails);
assemblyEngine.setRecoverDanglingHeads(recoverDanglingHeads);
assemblyEngine.setMinBaseQualityToUseInAssembly(MIN_BASE_QUALTY_SCORE);

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -346,7 +346,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
Assert.assertFalse(lineIteratorAnn.hasNext());
}
@Test
@Test(enabled = false)
public void testQualByDepth() throws IOException {
/*
@ -373,16 +373,16 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
*/
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("b6e8ffdab100b0ea1f8cb89e6e29a9ed"));
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("707be4798b1e14e3d6827a49104be120"));
final File outputVCF = executeTest("testQualByDepth", spec).getFirst().get(0);
final String baseNoQD = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -XA QualByDepth";
final WalkerTestSpec specNoQD = new WalkerTestSpec(baseNoQD, 1, Arrays.asList("23785ea79ac6945d086cbf5613885881"));
final WalkerTestSpec specNoQD = new WalkerTestSpec(baseNoQD, 1, Arrays.asList("7e582b422a5de47706daefaae17b8245"));
specNoQD.disableShadowBCF();
final File outputVCFNoQD = executeTest("testQualByDepth calling without QD", specNoQD).getFirst().get(0);
final String baseAnn = String.format("-T VariantAnnotator -R %s -V %s", REF, outputVCFNoQD.getAbsolutePath()) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -A QualByDepth";
final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("4ccdbebcfd02be87ae5b4ad94666f011"));
final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("cc4e2b12872b2b25ab1c106516b2ac6a"));
specAnn.disableShadowBCF();
final File outputVCFAnn = executeTest("testQualByDepth re-annotation of QD", specAnn).getFirst().get(0);

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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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, "50323a284788c8220c9226037c7003b5"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d5980df681bc57e10c681901494b46d2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "19efc8020f31d1b68d80c50df0629e50"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "bb6c326616790076de5111a7a3f6feb5"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "06d37e116871d8840d3de17a51049363"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "53517b967a60d800a9d9d1d5a1bc54c9"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "39bf5fe3911d0c646eefa8f79894f4df"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "d926d653500a970280ad7828d9ee2b84"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "83ddc16e4f0900429b2da30e582994aa"});
@ -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("4e2c20650c4c5ae6fa44b289eae5771d"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7c263d77bf831551366c6e36233b46ce"));
spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}

24
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -84,7 +84,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "489073bf0034fe9f10e6472ab93a17eb");
HCTest(CEUTRIO_BAM, "", "9e90f4ed1a04ce159ad3e560e62f5d6b");
}
@Test
@ -104,7 +104,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerGraphBasedMultiSample() {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "891295d8795c0ac894a2aec873e2a1d4");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "8d1edb0ea25c55a8c825b4e1470e219f");
}
@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",
"a1e59313516c2d5eeedae8348b0bdff1");
"d734a90b07dd0d6b051b7c0961787f98");
}
@Test
@ -178,7 +178,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("763d4d8d84a4080db18235a413478660"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@ -199,7 +199,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestDanglingTailMergingForDeletions() throws IOException {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800";
final String base = String.format("-T HaplotypeCaller -recoverDanglingTails --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
final File outputVCF = executeTest("HCTestDanglingTailMergingForDeletions", spec).getFirst().get(0);
@ -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("2b240d51aa9b0d1f65f4e899a2feb97e"));
Arrays.asList("32af503f1d58b1f34d896ea2ddb891aa"));
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("d2bb1a904ad419c565b00c3ac98048d1"));
Arrays.asList("39519c4f07d229f266430a0b0cfdf1db"));
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("73c52372a1a80f052ea2b728ee17bf22"));
Arrays.asList("d1e1de9f1d33c8c3f96520d674c76cda"));
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("1b41bf83b9c249a9a5fffb1e308668c1"));
Arrays.asList("10363ebae7edb0e81c2e668f7dbfba15"));
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("dbe5ef6ce1a9015ff4318691f5f45fda"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("4eb63e603e7a99388bb421591350de8c"));
spec.disableShadowBCF();
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
}
@ -313,7 +313,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testMissingKeyAlternativeHaplotypesBugFix() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header ",
b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e33053579a21d4cb23ba84107595891f"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6c70b7a52803f0bcfc53a14b894834df"));
spec.disableShadowBCF();
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
}
@ -323,7 +323,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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("0f6384c8e170840ef1490d262ac2e06e"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("0626e4c7543acc0cbb06c34435a2b730"));
spec.disableShadowBCF();
executeTest("testBadLikelihoodsDueToBadHaplotypeSelectionFix", spec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
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@ -60,7 +60,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
List<Object[]> tests = new ArrayList<>();
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, "fd9324a574f9204f7308fc1af422fdcc"});
tests.add(new Object[]{nct, "b0404b464097d667843da057bdc53c40"});
}
return tests.toArray(new Object[][]{});