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Merge pull request #674 from broadinstitute/rp_improve_genotyping 

Improvements to genotyping accuracy.
This commit is contained in:
Ryan Poplin 2014-07-09 16:03:09 -04:00
parent a85bc0b577 74a7674d70
commit 5eee065133
7 changed files with 66 additions and 54 deletions
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4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -385,8 +385,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
* from another location in the genome. Suppose a read has many mismatches from the reference, say like 5, but
* has a very high mapping quality of 60. Without this parameter, the read would contribute 5 * Q30 evidence
* in favor of its 5 mismatch haplotype compared to reference, potentially enough to make a call off that single
* read for all of these events. With this parameter set to Q30, though, the maximum evidence against the reference
* that this (and any) read could contribute against reference is Q30.
* read for all of these events. With this parameter set to Q30, though, the maximum evidence against any haplotype
* that this (and any) read could contribute is Q30.
*
* Set this term to any negative number to turn off the global mapping rate
*/

36
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -74,6 +74,7 @@ import java.util.*;
public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeCallerArgumentCollection> {
private final static List<Allele> NO_CALL = Collections.singletonList(Allele.NO_CALL);
private final static int ALLELE_EXTENSION = 2;
private MergeVariantsAcrossHaplotypes crossHaplotypeEventMerger;
@ -170,7 +171,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
* @param activeRegionWindow Active window
* @param genomeLocParser GenomeLocParser
* @param activeAllelesToGenotype Alleles to genotype
* @param emitReferenceConfidence whether we should add a &lt;NON_REF&gt; alternative allele to the result variation contexts.
* @param emitReferenceConfidence whether we should add a <NON_REF></NON_REF> alternative allele to the result variation contexts.
*
* @return A CalledHaplotypes object containing a list of VC's with genotyped events and called haplotypes
*
@ -249,7 +250,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
if (logger != null) logger.info("Genotyping event at " + loc + " with alleles = " + mergedVC.getAlleles());
}
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap = convertHaplotypeReadMapToAlleleReadMap(haplotypeReadMap, alleleMapper, configuration.getSampleContamination());
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap = convertHaplotypeReadMapToAlleleReadMap(haplotypeReadMap, alleleMapper, configuration.getSampleContamination(), genomeLocParser, mergedVC);
if (emitReferenceConfidence) addMiscellaneousAllele(alleleReadMap);
@ -257,7 +258,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
final VariantContext call = calculateGenotypes(null, null, null, null, new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), calculationModel, false, null);
if( call != null ) {
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap_annotations = ( configuration.USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ? alleleReadMap :
convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, emptyDownSamplingMap ) );
convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, emptyDownSamplingMap, genomeLocParser, null ) );
if (emitReferenceConfidence) addMiscellaneousAllele(alleleReadMap_annotations);
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = addFilteredReadList(genomeLocParser, alleleReadMap_annotations, perSampleFilteredReadList, call, true);
@ -489,10 +490,23 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
haplotypes.removeAll(haplotypesToRemove);
}
// BUGBUG: ugh, too complicated
/**
* The reads, partioned by haplotype, must now be partioned by alleles.
* That is, some alleles are supported by multiple haplotypes and we marginalize over them by taking the max likelihood.
* In addition we subset down to only reads which overlap the alleles (plus a small extension)
* @param haplotypeReadMap Map from reads -> (haplotypes, likelihoods)
* @param alleleMapper Map from alleles -> list of haplotypes which support that allele
* @param perSampleDownsamplingFraction Map from samples -> downsampling fraction
* @param genomeLocParser a genome loc parser
* @param eventsToGenotype the alleles to genotype in a single VariantContext, will be null if we don't want to require overlap
* @return Map from reads -> (alleles, likelihoods)
*/
protected Map<String, PerReadAlleleLikelihoodMap> convertHaplotypeReadMapToAlleleReadMap( final Map<String, PerReadAlleleLikelihoodMap> haplotypeReadMap,
final Map<Allele, List<Haplotype>> alleleMapper,
final Map<String,Double> perSampleDownsamplingFraction ) {
final Map<String,Double> perSampleDownsamplingFraction,
final GenomeLocParser genomeLocParser,
final VariantContext eventsToGenotype) {
final GenomeLoc callLoc = ( eventsToGenotype != null ? genomeLocParser.createGenomeLoc(eventsToGenotype) : null );
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap = new LinkedHashMap<>();
for( final Map.Entry<String, PerReadAlleleLikelihoodMap> haplotypeReadMapEntry : haplotypeReadMap.entrySet() ) { // for each sample
@ -500,13 +514,15 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
for( final Map.Entry<Allele, List<Haplotype>> alleleMapperEntry : alleleMapper.entrySet() ) { // for each output allele
final List<Haplotype> mappedHaplotypes = alleleMapperEntry.getValue();
for( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> readEntry : haplotypeReadMapEntry.getValue().getLikelihoodReadMap().entrySet() ) { // for each read
double maxLikelihood = Double.NEGATIVE_INFINITY;
for( final Map.Entry<Allele,Double> alleleDoubleEntry : readEntry.getValue().entrySet() ) { // for each input allele
if( mappedHaplotypes.contains( new Haplotype(alleleDoubleEntry.getKey())) ) { // exact match of haplotype base string
maxLikelihood = Math.max( maxLikelihood, alleleDoubleEntry.getValue() );
if( eventsToGenotype == null || callLoc.overlapsP(genomeLocParser.createPaddedGenomeLoc(genomeLocParser.createGenomeLocUnclipped(readEntry.getKey()), ALLELE_EXTENSION)) ) { // make sure the read overlaps
double maxLikelihood = Double.NEGATIVE_INFINITY;
for( final Map.Entry<Allele,Double> alleleDoubleEntry : readEntry.getValue().entrySet() ) { // for each input allele
if( mappedHaplotypes.contains( new Haplotype(alleleDoubleEntry.getKey())) ) { // exact match of haplotype base string
maxLikelihood = Math.max( maxLikelihood, alleleDoubleEntry.getValue() );
}
}
perReadAlleleLikelihoodMap.add(readEntry.getKey(), alleleMapperEntry.getKey(), maxLikelihood);
}
perReadAlleleLikelihoodMap.add(readEntry.getKey(), alleleMapperEntry.getKey(), maxLikelihood);
}
}
perReadAlleleLikelihoodMap.performPerAlleleDownsampling(perSampleDownsamplingFraction.get(haplotypeReadMapEntry.getKey())); // perform contamination downsampling

22
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
View File

@ -274,7 +274,6 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
// a new read/allele map, to contain the uncapped reads, haplotypes, and potentially the capped reference log10ls
final PerReadAlleleLikelihoodMap processedReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
Allele refAllele = null;
final int numReads = reads.size();
for (int readIndex = 0; readIndex < numReads; readIndex++) {
@ -283,33 +282,30 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
final GATKSAMRecord originalRead = reads.get(readIndex);
final GATKSAMRecord processedRead = processedReads.get(readIndex);
// keep track of the reference likelihood and the best non-ref likelihood
double refLog10l = Double.NEGATIVE_INFINITY;
double bestNonReflog10L = Double.NEGATIVE_INFINITY;
for ( Allele allele : alleleHaplotypeMap.keySet() ) {
for ( final Allele allele : alleleHaplotypeMap.keySet() ) {
final double log10l = perReadAlleleLikelihoodMap.getLikelihoodAssociatedWithReadAndAllele(processedRead, allele);
final Haplotype haplotype = alleleHaplotypeMap.get(allele);
if ( haplotype.isNonReference() )
bestNonReflog10L = Math.max(bestNonReflog10L, log10l);
else {
refAllele = allele;
refLog10l = log10l;
}
writeDebugLikelihoods(processedRead, haplotype, log10l);
// add the ORIGINAL (non-capped) read to the final map, along with the current haplotype and associated log10l
processedReadAlleleLikelihoodMap.add(originalRead, allele, log10l);
}
// ensure that the reference haplotype is no worse than the best non-ref haplotype minus the global
// ensure that any haplotype is no worse than the best non-ref haplotype minus the global
// mismapping rate. This protects us from the case where the assembly has produced haplotypes
// that are very divergent from reference, but are supported by only one read. In effect
// we capping how badly scoring the reference can be for any read by the chance that the read
// we capping how badly scoring any haplotype can be for any read by the chance that the read
// itself just doesn't belong here
final double worstRefLog10Allowed = bestNonReflog10L + log10globalReadMismappingRate;
if ( refLog10l < (worstRefLog10Allowed) ) {
processedReadAlleleLikelihoodMap.add(originalRead, refAllele, worstRefLog10Allowed);
final double worstAllowedLog10l = bestNonReflog10L + log10globalReadMismappingRate;
for ( final Allele allele : alleleHaplotypeMap.keySet() ) {
final double log10l = perReadAlleleLikelihoodMap.getLikelihoodAssociatedWithReadAndAllele(processedRead, allele);
if( log10l < worstAllowedLog10l ) {
processedReadAlleleLikelihoodMap.add(originalRead, allele, worstAllowedLog10l);
}
}
}
return processedReadAlleleLikelihoodMap;

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

@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "c2a6bd61aee2edab2439eeb14bdc1aeb");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "b9a5d461e4bc93742ab741f491780438");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -88,13 +88,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"f23ac8256edfdf949cefcb245c227abb");
"d57fd9e174361c386084786976df4872");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"40ef4d4188d326ca0d4e29f4de4b53ff");
"b63bf0f2848f28e52fd5c7621bbd27c7");
}
private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@ -106,7 +106,7 @@ 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",
"e328436354bdf7604d987c6e2c9172eb");
"972a726b0ba476f6215bf162439db2cd");
}
}

16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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@ -67,12 +67,12 @@ 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, "afb1c0ff2556b01ee03596b19bfc60bd"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "dad32e660bf4bffcb0f996d9f3fd5073"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "d4a44ce515fdbfa2017b7bd08dcddadc"});
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"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "662481d96a58c5475dc4752466a8d3b2"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d9f7fd119eec40b4610cb4aae1cbed75"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cbf6d876045051a68aca784491cca6cf"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5c07fa3edca496a84fd17cecad06230"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "330685c734e277d70a44637de85ad54d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e6ec90da053a612f0c615e221eb34baa"});
return tests.toArray(new Object[][]{});
}
@ -137,7 +137,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testWrongGVCFNonVariantRecordOrderBugFix() {
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, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e286b5eb72e3f75e7b08e5729cdfe019"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5fbc88cf1136212afac1fd0b7e0e8ce8"));
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@ -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("f70f418ba99bbd82f74dc85afb02bca4"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("1b77bc92962fa10b5eec86fe9400c528"));
spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}

32
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -84,17 +84,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "80e190483299828700dd04c221111b5c");
HCTest(CEUTRIO_BAM, "", "b66f8d08e0b94ddc52bd06dadbb9b299");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "6632475b1cefce9a0c5727bc919501e5");
HCTest(NA12878_BAM, "", "42de756c08b028be70287ada1022526e");
}
@Test
public void testHaplotypeCallerMinBaseQuality() {
HCTest(NA12878_BAM, "-mbq 15", "31fe63ea44407b6aa40261319a414488");
HCTest(NA12878_BAM, "-mbq 15", "f753c9e284eafb1424b7f9d88193fdee");
}
@Test
@ -104,7 +104,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerGraphBasedMultiSample() {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "b8307688564f0735f630170d8e655a58");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "f200260127d0f63cc61ce5f2287bd5a0");
}
@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",
"fd3b7ac0cc8c3a727cf0e5783645ca28");
"4b1271aaa70f46ed6c987cdf4610b7f0");
}
@Test
@ -131,7 +131,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "ec77ac891cac9461b2eb011270166dc1");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "575850d9a8195000a2ef747f838aaf77");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -168,7 +168,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "59e0f10f8822e2a5e7d2fabb71dbea3f");
HCTestNearbySmallIntervals(NA12878_BAM, "", "f1c19db6fb896332de232b7e5cbc2016");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -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("923fee5e23930e0b321258d6d3fa2ffe"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("b484c2e943d3f1f3248947726fd60cdb"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@ -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("dc3c63e1e131806fe5455ad0286bebab"));
Arrays.asList("cf314806fcb0847e2ed99c7013e5d55d"));
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("69ece81900b78a3d2712898c99e15d75"));
Arrays.asList("0e68c82163d4fee30b4135d4ebd1a3ba"));
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("f369423c10d3aece3ef5e4655bd3af55"));
Arrays.asList("be7bf9e8f78d6a9ee569b750054991ac"));
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("dad6d8c007822883e230eb4250b8b788"));
Arrays.asList("01b716d421dc33f7a6bc8c387b7e3322"));
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("47c53227ca7be6b343a9900e61594281"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("f2deea31d32c0cfe3298755a83171c8f"));
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("e613c8a2f637cff3e049de34c354edde"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cd33c69a34a66b5baca72841fe8a2bc0"));
spec.disableShadowBCF();
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
}
@ -336,9 +336,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
// but please make sure that both outputs get the same variant,
// alleles all with DBSNP ids
// We test here that change in active region size does not have an effect in placement of indels.
final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList("8512638ddb84eec5f58eaa1be6f58401"));
final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList("0f87fd95350fade475fe3c5df8dd9e08"));
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList("9645d154812ae4db5357e7e5628936ab"));
final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList("b3a2853d51a7817999a3be8e72d9ac23"));
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::longInterval",longSpec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
View File

@ -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, "31a7bb9fb5bc512120b88c5ecdd81139"});
tests.add(new Object[]{nct, "a2718251ffae9db885b7f74b33dd5b57"});
}
return tests.toArray(new Object[][]{});