Merge pull request #478 from broadinstitute/eb_generalize_hc_values_as_args
Pulled out some hard-coded values from the read-threading and isActive c...
This commit is contained in:
Ryan Poplin
commit
bdd06ebfc2
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@ -341,6 +341,12 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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// general advanced arguments to control haplotype caller behavior
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// -----------------------------------------------------------------------------------------------
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/**
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* The minimum confidence needed for a given base for it to be used in variant calling.
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*/
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@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
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public byte MIN_BASE_QUALTY_SCORE = 10;
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/**
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* Users should be aware that this argument can really affect the results of the variant calling and should exercise caution.
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* Using a prune factor of 1 (or below) will prevent any pruning from the graph which is generally not ideal; it can make the
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@ -440,10 +446,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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@Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="If specified, we will write DOT formatted graph files out of the assembler for only this graph size", required = false)
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protected boolean debugGraphTransformations = false;
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@Hidden // TODO -- not currently useful
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@Argument(fullName="useLowQualityBasesForAssembly", shortName="useLowQualityBasesForAssembly", doc="If specified, we will include low quality bases when doing the assembly", required = false)
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protected boolean useLowQualityBasesForAssembly = false;
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@Hidden
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@Argument(fullName="dontTrimActiveRegions", shortName="dontTrimActiveRegions", doc="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping", required = false)
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protected boolean dontTrimActiveRegions = false;
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@ -536,10 +538,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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private final static int maxReadsInRegionPerSample = 1000; // TODO -- should be an argument
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private final static int minReadsPerAlignmentStart = 5; // TODO -- should be an argument
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// bases with quality less than or equal to this value are trimmed off the tails of the reads
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private static final byte MIN_TAIL_QUALITY = 20;
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private byte MIN_TAIL_QUALITY;
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private static final byte MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION = 6;
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// the minimum length of a read we'd consider using for genotyping
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private final static int MIN_READ_LENGTH = 10;
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@ -651,9 +652,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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assemblyEngine.setDebugGraphTransformations(debugGraphTransformations);
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assemblyEngine.setAllowCyclesInKmerGraphToGeneratePaths(allowCyclesInKmerGraphToGeneratePaths);
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assemblyEngine.setRecoverDanglingTails(!dontRecoverDanglingTails);
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assemblyEngine.setMinBaseQualityToUseInAssembly(MIN_BASE_QUALTY_SCORE);
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MIN_TAIL_QUALITY = (byte)(MIN_BASE_QUALTY_SCORE - 1);
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if ( graphWriter != null ) assemblyEngine.setGraphWriter(graphWriter);
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if ( useLowQualityBasesForAssembly ) assemblyEngine.setMinBaseQualityToUseInAssembly((byte)1);
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// setup the likelihood calculation engine
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if ( phredScaledGlobalReadMismappingRate < 0 ) phredScaledGlobalReadMismappingRate = -1;
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@ -758,12 +761,12 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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final GenotypesContext genotypes = GenotypesContext.create(splitContexts.keySet().size());
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final MathUtils.RunningAverage averageHQSoftClips = new MathUtils.RunningAverage();
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for( final Map.Entry<String, AlignmentContext> sample : splitContexts.entrySet() ) {
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final double[] genotypeLikelihoods = referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(sample.getValue().getBasePileup(), ref.getBase(), (byte) 18, averageHQSoftClips).genotypeLikelihoods;
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final double[] genotypeLikelihoods = referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(sample.getValue().getBasePileup(), ref.getBase(), MIN_BASE_QUALTY_SCORE, averageHQSoftClips).genotypeLikelihoods;
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genotypes.add( new GenotypeBuilder(sample.getKey()).alleles(noCall).PL(genotypeLikelihoods).make() );
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}
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final List<Allele> alleles = Arrays.asList(FAKE_REF_ALLELE , FAKE_ALT_ALLELE);
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final VariantCallContext vcOut = UG_engine_simple_genotyper.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getStop(), alleles).genotypes(genotypes).make(), GenotypeLikelihoodsCalculationModel.Model.INDEL);
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final VariantCallContext vcOut = UG_engine_simple_genotyper.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getStop(), alleles).genotypes(genotypes).make(), GenotypeLikelihoodsCalculationModel.Model.SNP);
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final double isActiveProb = vcOut == null ? 0.0 : QualityUtils.qualToProb( vcOut.getPhredScaledQual() );
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return new ActivityProfileState( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > 6.0 ? ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileState.Type.NONE, averageHQSoftClips.mean() );
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@ -1113,8 +1116,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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GATKSAMRecord clippedRead;
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if (errorCorrectReads)
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clippedRead = ReadClipper.hardClipLowQualEnds( myRead, MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION );
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else if (useLowQualityBasesForAssembly)
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clippedRead = myRead;
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else // default case: clip low qual ends of reads
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clippedRead= ReadClipper.hardClipLowQualEnds( myRead, MIN_TAIL_QUALITY );
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@ -358,7 +358,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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final File outputVCFNoQD = executeTest("testQualByDepth calling without QD", specNoQD).getFirst().get(0);
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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";
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final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("0c331915b07b42d726bc3d623aa9997b"));
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final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("b171258ed3ef5ae0d6c21fe04e5940fc"));
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specAnn.disableShadowBCF();
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final File outputVCFAnn = executeTest("testQualByDepth re-annotation of QD", specAnn).getFirst().get(0);
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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", "", "ff19ae39b0695680ea670d53f6f9ce47");
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "b5cd204b9dd6a5210b49d91186cf2b1d");
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}
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private void HCTestSymbolicVariants(String bam, String args, String md5) {
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@ -88,12 +88,12 @@ 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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"b787be740423b950f8529ccc838fabdd");
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"cdf6d200324949a3484668774d2289d7");
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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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"f74d68cbc1ecb66a7128258e111cd030");
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"ccc3864207d700c00238066ec5ae33c5");
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}
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}
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@ -65,13 +65,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
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final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
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// this functionality can be adapted to provide input data for whatever you might want in your data
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "96328c91cf9b06de231b37a22a7a7639"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ac25e9a78b89655197513bb0eb7a6845"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "dc0dde72131d562587acae967cf2031f"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.NONE, WExIntervals, "7cb1e431119df00ec243a6a115fa74b8"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "90e22230149e6c32d1115d0e2f03cab1"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.GVCF, WExIntervals, "b39a4bc19a0acfbade22a011cd229262"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "53aa13711a1ceec1453f21c705723f04"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "4bb8e44b2d04757f8b11ca6400828357"});
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tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "8ddc291584f56e27d125b6a0523f2703"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.NONE, WExIntervals, "39bf5fe3911d0c646eefa8f79894f4df"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "e53e164cc3f5cbd5fba083f2cdb98a88"});
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tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.GVCF, WExIntervals, "a258dbbfabe88dad11d57151cd256831"});
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return tests.toArray(new Object[][]{});
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}
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@ -84,22 +84,27 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMultiSample() {
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HCTest(CEUTRIO_BAM, "", "f2ad35b5e0d181fb18da86a8971ce4f4");
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HCTest(CEUTRIO_BAM, "", "abbfdcbf4bfed7547a48121091a7e16f");
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}
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@Test
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public void testHaplotypeCallerSingleSample() {
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HCTest(NA12878_BAM, "", "06abde3268336a7cdb21970f12e819ba");
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HCTest(NA12878_BAM, "", "96f299a5cf411900b8eda3845c3ce465");
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}
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@Test
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public void testHaplotypeCallerMinBaseQuality() {
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HCTest(NA12878_BAM, "-mbq 15", "6509cfd0554ecbb92a1b303fbcc0fcca");
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}
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@Test
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public void testHaplotypeCallerGraphBasedSingleSample() {
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HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "3d1cb9acdf66547f88ad1742e8178044");
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HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "83fe0694621bc1e0240f6f79eb6d6999");
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}
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@Test
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public void testHaplotypeCallerGraphBasedMultiSample() {
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HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "af6f1f504ad771201aedc0157de8830a");
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HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "8b75034f9aa8435962da98eb521c8f0b");
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}
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@Test(enabled = false) // can't annotate the rsID's yet
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@ -110,7 +115,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMultiSampleGGA() {
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HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
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"fd43de437bbaf960499f67daedc6ef63");
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"fc271f21c0693e4fa6394e27d722fb52");
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}
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@Test
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@ -126,7 +131,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerSingleSampleIndelQualityScores() {
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HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3a3bb5f0bcec603287520841c559638f");
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HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "d3fc49d3d3c8b6439548133e03faa540");
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}
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private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
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@ -163,7 +168,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerNearbySmallIntervals() {
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HCTestNearbySmallIntervals(NA12878_BAM, "", "75820a4558a559b3e1636fdd1b776ea2");
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HCTestNearbySmallIntervals(NA12878_BAM, "", "a415bc76231a04dc38412ff38aa0dc49");
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}
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// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
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@ -173,7 +178,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void HCTestProblematicReadsModifiedInActiveRegions() {
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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";
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final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("170896ddcfe06ec47e08aefefd99cf78"));
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final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("763d4d8d84a4080db18235a413478660"));
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executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
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}
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@ -222,7 +227,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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public void HCTestReducedBam() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
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Arrays.asList("277aa95b01fa4d4e0086a2fabf7f3d7e"));
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Arrays.asList("12c56262ed30db1249b8d722e324357c"));
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executeTest("HC calling on a ReducedRead BAM", spec);
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}
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@ -230,7 +235,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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public void testReducedBamWithReadsNotFullySpanningDeletion() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
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Arrays.asList("6a9222905c740b9208bf3c67478514eb"));
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Arrays.asList("1627cf5f3a97e8b73b3c095db46aef1b"));
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executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
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}
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@ -244,7 +249,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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public void HCTestDBSNPAnnotationWGS() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-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,
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Arrays.asList("6ab05a77d2e79d21ba85fadf844a13ba"));
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Arrays.asList("51e63c0431817ca1824b01e56341a8ae"));
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executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
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}
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@ -253,7 +258,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
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+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
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Arrays.asList("1352cbe1404aefc94eb8e044539a9882"));
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Arrays.asList("e39c73bbaf22b4751755d9f5bb2a8d3d"));
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executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
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}
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@ -261,7 +266,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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public void HCTestDBSNPAnnotationWGSGraphBased() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-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,
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Arrays.asList("903af86b396ce88a6c8e4f4016fbe769"));
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Arrays.asList("a2ada5984fe835f7f2169f8393d122a6"));
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executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
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}
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@ -270,7 +275,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
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+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
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Arrays.asList("69db1045b5445a4f90843f368bd62814"));
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Arrays.asList("c14d7f23dedea7e7ec99a90843320c1a"));
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executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
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}
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@ -293,7 +298,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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public void HCTestAggressivePcrIndelModelWGS() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-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,
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Arrays.asList("824188743703bc09225c5b9c6b404ac1"));
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Arrays.asList("ee73759f4372df678e7aa97346d87a70"));
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executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
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}
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@ -301,7 +306,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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public void HCTestConservativePcrIndelModelWGS() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-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,
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Arrays.asList("14de866430f49c0026aafc1e34ed8250"));
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Arrays.asList("a9fa660910bf5e35267475f3b2d75766"));
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executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -61,7 +61,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
|
|||
List<Object[]> tests = new ArrayList<>();
|
||||
|
||||
for ( final int nct : Arrays.asList(1, 2, 4) ) {
|
||||
tests.add(new Object[]{nct, "29cb04cca87f42b4762c34dfea5d15b7"});
|
||||
tests.add(new Object[]{nct, "1f463bf3a06c401006858bc446ecea54"});
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
|
|
|
|||
Loading…
Reference in New Issue