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Initialize annotations so that --disableDithering actually works

This commit is contained in:
Laura Gauthier 2015-04-01 20:17:03 -04:00
parent 761e456d07
commit 9c842df3a3
4 changed files with 56 additions and 53 deletions
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3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -828,6 +828,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
vcfWriter.writeHeader(new VCFHeader(headerInfo, sampleSet));
//now that we have all the VCF headers, initialize the annotations (this is particularly important to turn off RankSumTest dithering in integration tests)
annotationEngine.invokeAnnotationInitializationMethods(headerInfo);
try {
// fasta reference reader to supplement the edges of the reference sequence
referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "329e57675a6bab117597f02e3f109095");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "070729585401dda47838911928ffbd2f");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -96,13 +96,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"4c12c04c34c782b25df78d37868e742d");
"64421f715e0258defc9efcfef56bdaab");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"c3fc8876b9b7247f68d758b8a9d60fe5");
"d2306f6ecfcee9340423ba251e0736a3");
}
private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@ -114,7 +114,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
"b6576ef09027cb22fa02efda67f7139d");
"22c4135a87be18940ff622ea7ff9cabc");
}
}

48
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -75,12 +75,12 @@ 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, "6bfe8418aefa0d5d04bdc8f5f31bbb97"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8daf142d0f42967b9c59aae4580a18c5"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1ad6d0d5764e2bc0839af4b79f1bd351"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "00aa548e22334fc121f0c8bee2b05d7a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2e64530bfc8cb0a3ad72cc5d11d4694b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "c236b1f6bfbbbc258d3077d75bb9e552"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3e440b1b755a21d7bd3ecb093af8f43e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ebe078a1e209a5b231aeeba6deebcb8a"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b6d3cbc4eecb8d295898d94335be54c2"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ca1e6cb78157273a4a96ba00e6d4713"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8645c191ca5dbbae8dcb1389717f985a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "82f2efd1e9ec6197344d9001b653c7fb"});
return tests.toArray(new Object[][]{});
}
@ -94,13 +94,13 @@ 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, "58abeeaebe89fa5e65bae305f5325a13"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ba349abd7370252215ebf9e2f246283c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c91ff30df7644c3fd5be1355533d9fef"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "04d025e1102bede70d0aa9dc25a89e01"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a1fcce758ed1bd8ead5030b598fd66eb"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "92c7415dd1a5793161032d839b88fc28"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b90d7c900ff4a8b5e58d6bd4ad64d750"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "7abdd32f0d11cbf43f5bceeca946a428"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "7e84e4562d8df6e593e58f017f697355"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "307ce5ada7c68e2f08664937bafa6281"});
final String NA12878bandedResolutionMD5 = "12ce2c83d71ad3db7269c22e65a47ffb";
final String NA12878bandedResolutionMD5 = "74f728f1c42e3014776197606ddf5116";
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@ -117,12 +117,12 @@ 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, "e85d74be34c91ab84ea1e6ab6276fbab"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "10dd974f0fd83b8f187e1e9f39ba9237"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fc7ae67b25ff3e82062b80827bd30f6d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "87a745384652813976ee37091be45a14"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a36a9f819e82f7ba6d77ab0b65475fbc"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "bbd62dbeddfdc7353264870e4379cc04"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "f441aab92b07591281fa44748b7bd71e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d54d7988552a13de90977ba06b094b74"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a1e2f104c50c89b9c562045daebf07ca"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "91164cf1247f5b187ad133b280aa1fd2"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "b5c1b79550a8d8bb479895e2be38d945"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "48b737b4f1739edd275eb347c6ca5997"});
return tests.toArray(new Object[][]{});
}
@ -135,12 +135,12 @@ 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, "7f1b295150967269545096564d5ebcca"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "97c5a77752305990420d5d725c70c2cd"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "04b5f3f7a6d1c53beef14c8b295883b1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "f0b3e472e175ffa4fdf4e04f88e0ade1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "747204e4bad4620c5298b683813c65ee"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "5a2d32868f007d9d3537ee9d66bd6f38"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "081d943a092b7ad71d1f1fa6ec191ace"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "93f95c7a51741f8e527f1308ffd91052"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a6e858123e40efece5a9a43a0c05bdb2"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "3d8f4f849df0b9cddb1ec61279e91a83"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1fbe1435b860400ecae3115141453c9a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "af7f383fd675d2edfaba7f67a96e67c7"});
return tests.toArray(new Object[][]{});
}

50
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -96,82 +96,82 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "", "6d8a38310a086f4d80f25d2b80a309b2");
HCTest(CEUTRIO_BAM, "", "e8a73b950d027239b780757d898c7334");
}
@Test
public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "93990d0fed73087294548e71c4e661e9");
HCTest(NA12878_BAM, "", "c741efeb6f3e412c4e707da3cabee621");
}
@Test
public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-ploidy 1", "deac83402aa9ef26fcc42e5ab08140d3");
HCTest(CEUTRIO_BAM, "-ploidy 1", "5bfcfdea258a3dafa04a99dd2b000c87");
}
@Test
public void testHaplotypeCallerSingleSampleHaploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 1", "633d7bd09d202b062854a647ec0f3ce0");
HCTest(NA12878_BAM, "-ploidy 1", "304d2ade384406342655fdfd445576a3");
}
@Test
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "605498f14cb0b01695109035068a147e");
HCTest(NA12878_BAM, "-ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c");
}
@Test
public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "93990d0fed73087294548e71c4e661e9");
HCTest(NA12878_BAM, "-mbq 15", "c741efeb6f3e412c4e707da3cabee621");
}
@Test
public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "633d7bd09d202b062854a647ec0f3ce0");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "304d2ade384406342655fdfd445576a3");
}
@Test
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "605498f14cb0b01695109035068a147e");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c");
}
@Test
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "1bd3336031e18c5f06abe760c33dd6be");
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ffd2363d2f7afd694b8e9b23c51b0cea");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "e4a2b4c7adc7d45e2ad2bb61d263b9ac");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "ab1630552bcc0a46431b3f6b7bd50bb5");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "dc757f57a6ddac88ddceab5be1533f89");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "31a21023efaf6f030478e5542ec652fe");
}
@Test
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "c68a0659d6de9fb1c2f8e2db4da2f8a2");
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "1c91ca0c8c04cbce1ace3e9884efd458");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
"469228219a10f003e558aae66a838e73");
"2944a830504b4e0b87bb8babc8ea39ae");
}
@Test
public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"535cde1cbefd5b90cae793cbbdce5893");
"b4da788ff173453d915a807149d9ab5d");
}
@Test
public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"d8705ab5f7d4532c2ff8063244a72788");
"7a3a8a81c3f984d74e6e3e35f5e62aa3");
}
@Test
@ -187,7 +187,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "a139a6d01101064a4a093b24449d8b52");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "60df4797f86c1454c0eb76c5eaf2ad38");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -224,7 +224,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "f6fe463f338f6c5133ba08f1d667c23e");
HCTestNearbySmallIntervals(NA12878_BAM, "", "7af25494bf2b05cc838ebf7055407c30");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -234,7 +234,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, 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("869e786baa1a72a08f0a3781804abb3e"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3f01b3be2004f784a0fddc9e63aeba2a"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@ -296,7 +296,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("2dc24f409ec1aa402ad892dffe317618"));
Arrays.asList("e894e9f50112edad270f36f78e76a8e3"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -305,7 +305,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("a2f40779558c1157353c6fcfd3783a76"));
Arrays.asList("9e384f2bd2eb7a6d5ee1685ab5e75501"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -313,7 +313,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGSGraphBased() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("9d7ab1c89cce238cff055dc5e9091fb1"));
Arrays.asList("801a3af44153deee939370dcaaa110ab"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -322,7 +322,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("b2240a53e441064a1a60e60de4ca49ad"));
Arrays.asList("efac9fd7e7a92e3f130e7db9cbff4a45"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -345,7 +345,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestAggressivePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("591f8f31524510ace882a860d6850871"));
Arrays.asList("c851be534595a2547a8ebf81f1b923d1"));
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
}
@ -353,7 +353,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestConservativePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("038db1cf0dadfe746a14e05f5cf3bb8e"));
Arrays.asList("95a3f339a15b1398cfc9f9e933999ea9"));
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
}
@ -446,6 +446,6 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "ab9907559e5b20dadbb6f24d02b8070c");
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "481787c9275ab9f2e2b53025805472b7");
}
}