Examples with SomaticVariant com.hartwig.hmftools.common.variant.SomaticVariant used on opensource projects

Example 1 with SomaticVariant

use of com.hartwig.hmftools.common.variant.SomaticVariant in project hmftools by hartwigmedical.

the class ConsequenceDeterminerTest method worksAsExpected.

@Test
public void worksAsExpected() {
    final SortedSetMultimap<String, GenomeRegion> regionMap = TreeMultimap.create();
    GenomeRegion testRegion = GenomeRegionFactory.create(CHROMOSOME, POSITION - 10, POSITION + 10);
    regionMap.put(testRegion.chromosome(), testRegion);
    final Slicer slicer = SlicerFactory.fromRegions(regionMap);
    final Map<String, HmfGenomeRegion> transcriptMap = Maps.newHashMap();
    transcriptMap.put(TRANSCRIPT, hmfRegion());
    final ConsequenceDeterminer determiner = new ConsequenceDeterminer(slicer, transcriptMap);
    final VariantConsequence rightConsequence = VariantConsequence.MISSENSE_VARIANT;
    final VariantConsequence wrongConsequence = VariantConsequence.OTHER;
    final ImmutableVariantAnnotation.Builder annotationBuilder = createVariantAnnotationBuilder().featureID(TRANSCRIPT).featureType(ConsequenceDeterminer.FEATURE_TYPE_TRANSCRIPT).gene(GENE).hgvsCoding(HGVS_CODING).hgvsProtein(HGVS_PROTEIN);
    final VariantAnnotation rightAnnotation = annotationBuilder.consequences(Lists.newArrayList(rightConsequence)).build();
    final VariantAnnotation wrongAnnotation = annotationBuilder.consequences(Lists.newArrayList(wrongConsequence)).build();
    final ImmutableSomaticVariantImpl.Builder variantBuilder = SomaticVariantTestBuilderFactory.create().chromosome(CHROMOSOME).ref(REF).alt(ALT).cosmicID(COSMIC_ID).totalReadCount(TOTAL_READ_COUNT).alleleReadCount(ALLELE_READ_COUNT);
    final SomaticVariant rightVariant = variantBuilder.position(POSITION).annotations(Lists.newArrayList(rightAnnotation)).build();
    final SomaticVariant wrongConsequenceVariant = variantBuilder.position(POSITION).annotations(Lists.newArrayList(wrongAnnotation)).build();
    final SomaticVariant wrongPositionVariant = variantBuilder.position(WRONG_POSITION).annotations(Lists.newArrayList(rightAnnotation)).build();
    final List<VariantReport> findings = determiner.run(Lists.newArrayList(rightVariant, wrongConsequenceVariant, wrongPositionVariant)).findings();
    assertEquals(1, findings.size());
    final VariantReport report = findings.get(0);
    assertEquals(GENE, report.gene());
    assertEquals(CHROMOSOME + ":" + POSITION, report.variant().chromosomePosition());
    assertEquals(REF, report.variant().ref());
    assertEquals(ALT, report.variant().alt());
    assertEquals(TRANSCRIPT + "." + TRANSCRIPT_VERSION, report.transcript());
    assertEquals(HGVS_CODING, report.hgvsCoding());
    assertEquals(HGVS_PROTEIN, report.hgvsProtein());
    assertEquals(rightConsequence.readableSequenceOntologyTerm(), report.consequence());
    assertEquals(COSMIC_ID, report.cosmicID());
    assertEquals(TOTAL_READ_COUNT, report.totalReadCount());
    assertEquals(ALLELE_READ_COUNT, report.alleleReadCount());
}

Example 2 with SomaticVariant

use of com.hartwig.hmftools.common.variant.SomaticVariant in project hmftools by hartwigmedical.

the class VariantAnalyzerTest method realCaseWorks.

@Test
public void realCaseWorks() {
    final GeneModel geneModel = new GeneModel(hmfRegions());
    final VariantAnalyzer analyzer = VariantAnalyzer.of(geneModel, testMicrosatelliteAnalyzer());
    final VariantAnnotation rightAnnotation = createVariantAnnotationBuilder(VariantConsequence.MISSENSE_VARIANT).featureType(RIGHT_FEATURE_TYPE).featureID(RIGHT_TRANSCRIPT).build();
    final VariantAnnotation wrongTranscript = createVariantAnnotationBuilder(VariantConsequence.MISSENSE_VARIANT).featureType(RIGHT_FEATURE_TYPE).featureID(WRONG_TRANSCRIPT).build();
    final VariantAnnotation wrongFeatureType = createVariantAnnotationBuilder(VariantConsequence.MISSENSE_VARIANT).featureType(WRONG_FEATURE_TYPE).featureID(RIGHT_TRANSCRIPT).build();
    final VariantAnnotation wrongConsequence = createVariantAnnotationBuilder(VariantConsequence.OTHER).featureType(RIGHT_FEATURE_TYPE).featureID(RIGHT_TRANSCRIPT).build();
    final List<SomaticVariant> variants = Lists.newArrayList(builder().position(420).annotations(Lists.newArrayList(rightAnnotation, wrongTranscript)).build(), builder().position(430).annotations(Lists.newArrayList(wrongConsequence)).build(), builder().position(440).annotations(Lists.newArrayList(wrongFeatureType)).build(), builder().position(460).annotations(Lists.newArrayList(rightAnnotation)).build());
    final VariantAnalysis analysis = analyzer.run(variants);
    assertEquals(4, analysis.passedVariants().size());
    assertEquals(3, analysis.mutationalLoad());
    assertEquals(1, analysis.findings().size());
}

Example 3 with SomaticVariant

use of com.hartwig.hmftools.common.variant.SomaticVariant in project hmftools by hartwigmedical.

the class ConsequenceDeterminer method toVariantReport.

@NotNull
private List<VariantReport> toVariantReport(@NotNull final List<SomaticVariant> variants) {
    final List<VariantReport> reports = Lists.newArrayList();
    for (final SomaticVariant variant : variants) {
        final ImmutableVariantReport.Builder builder = ImmutableVariantReport.builder();
        final VariantAnnotation variantAnnotation = findPrimaryRelevantAnnotation(variant, relevantTranscriptMap.keySet());
        // KODU: Variants with no relevant annotations should be filtered out by now.
        assert variantAnnotation != null;
        final HmfGenomeRegion hmfGenomeRegion = relevantTranscriptMap.get(variantAnnotation.featureID());
        assert hmfGenomeRegion != null;
        if (!variantAnnotation.gene().equals(hmfGenomeRegion.gene())) {
            LOGGER.warn("Annotated gene does not match gene expected from slicing annotation for " + variant);
        }
        if (!variantAnnotation.allele().equals(variant.alt())) {
            LOGGER.warn("Annotated allele does not match alt from variant for " + variant);
        }
        builder.variant(variant);
        builder.gene(variantAnnotation.gene());
        builder.transcript(hmfGenomeRegion.transcript());
        builder.hgvsCoding(variantAnnotation.hgvsCoding());
        builder.hgvsProtein(variantAnnotation.hgvsProtein());
        builder.consequence(variantAnnotation.consequenceString());
        final String cosmicID = variant.cosmicID();
        if (cosmicID != null) {
            builder.cosmicID(cosmicID);
        }
        builder.totalReadCount(variant.totalReadCount());
        builder.alleleReadCount(variant.alleleReadCount());
        reports.add(builder.build());
    }
    return reports;
}

Example 4 with SomaticVariant

use of com.hartwig.hmftools.common.variant.SomaticVariant in project hmftools by hartwigmedical.

the class LoadSomaticVariants method main.

public static void main(@NotNull final String[] args) throws ParseException, IOException, SQLException {
    final Options options = createBasicOptions();
    final CommandLine cmd = createCommandLine(args, options);
    final String vcfFileLocation = cmd.getOptionValue(VCF_FILE);
    final String highConfidenceBed = cmd.getOptionValue(HIGH_CONFIDENCE_BED);
    final String fastaFileLocation = cmd.getOptionValue(REF_GENOME);
    final String sample = cmd.getOptionValue(SAMPLE);
    final DatabaseAccess dbAccess = databaseAccess(cmd);
    final CompoundFilter filter = new CompoundFilter(true);
    if (cmd.hasOption(PASS_FILTER)) {
        filter.add(new PassingVariantFilter());
    }
    if (cmd.hasOption(SOMATIC_FILTER)) {
        filter.add(new SomaticFilter());
    }
    LOGGER.info("Reading somatic VCF File");
    final List<SomaticVariant> variants = SomaticVariantFactory.filteredInstance(filter).fromVCFFile(sample, vcfFileLocation);
    LOGGER.info("Reading high confidence bed file");
    final Multimap<String, GenomeRegion> highConfidenceRegions = BEDFileLoader.fromBedFile(highConfidenceBed);
    LOGGER.info("Loading indexed fasta reference file");
    IndexedFastaSequenceFile indexedFastaSequenceFile = new IndexedFastaSequenceFile(new File(fastaFileLocation));
    LOGGER.info("Querying purple database");
    final PurityContext purityContext = dbAccess.readPurityContext(sample);
    if (purityContext == null) {
        LOGGER.warn("Unable to retrieve purple data. Enrichment may be incomplete.");
    }
    final PurityAdjuster purityAdjuster = purityContext == null ? new PurityAdjuster(Gender.FEMALE, 1, 1) : new PurityAdjuster(purityContext.gender(), purityContext.bestFit().purity(), purityContext.bestFit().normFactor());
    final Multimap<String, PurpleCopyNumber> copyNumbers = Multimaps.index(dbAccess.readCopynumbers(sample), PurpleCopyNumber::chromosome);
    final Multimap<String, FittedRegion> copyNumberRegions = Multimaps.index(dbAccess.readCopyNumberRegions(sample), FittedRegion::chromosome);
    LOGGER.info("Incorporating purple purity");
    final PurityAdjustedSomaticVariantFactory purityAdjustmentFactory = new PurityAdjustedSomaticVariantFactory(purityAdjuster, copyNumbers, copyNumberRegions);
    final List<PurityAdjustedSomaticVariant> purityAdjustedVariants = purityAdjustmentFactory.create(variants);
    final double clonalPloidy = ClonalityCutoffKernel.clonalCutoff(purityAdjustedVariants);
    LOGGER.info("Enriching variants");
    final EnrichedSomaticVariantFactory enrichedSomaticVariantFactory = new EnrichedSomaticVariantFactory(highConfidenceRegions, indexedFastaSequenceFile, new ClonalityFactory(purityAdjuster, clonalPloidy), CanonicalTranscriptFactory.create(HmfGenePanelSupplier.allGeneList()));
    final List<EnrichedSomaticVariant> enrichedVariants = enrichedSomaticVariantFactory.enrich(purityAdjustedVariants);
    LOGGER.info("Persisting variants to database");
    dbAccess.writeSomaticVariants(sample, enrichedVariants);
    LOGGER.info("Complete");
}

Example 5 with SomaticVariant

use of com.hartwig.hmftools.common.variant.SomaticVariant in project hmftools by hartwigmedical.

the class PatientReporter method analyseGenomeData.

@NotNull
private GenomeAnalysis analyseGenomeData(@NotNull final String sample, @NotNull final String runDirectory) throws IOException {
    LOGGER.info(" Loading somatic snv and indels...");
    final List<SomaticVariant> variants = PatientReporterHelper.loadPassedSomaticVariants(sample, runDirectory);
    LOGGER.info("  " + variants.size() + " somatic passed snps, mnps and indels loaded for sample " + sample);
    LOGGER.info(" Analyzing somatic snp/mnp and indels....");
    final VariantAnalysis variantAnalysis = variantAnalyzer().run(variants);
    LOGGER.info(" Loading purity numbers...");
    final PurityContext context = PatientReporterHelper.loadPurity(runDirectory, sample);
    if (context.status().equals(FittedPurityStatus.NO_TUMOR)) {
        LOGGER.warn("PURPLE DID NOT DETECT A TUMOR. Proceed with utmost caution!");
    }
    final FittedPurity purity = context.bestFit();
    final FittedPurityScore purityScore = context.score();
    final List<PurpleCopyNumber> purpleCopyNumbers = PatientReporterHelper.loadPurpleCopyNumbers(runDirectory, sample);
    final List<GeneCopyNumber> panelGeneCopyNumbers = PatientReporterHelper.loadPurpleGeneCopyNumbers(runDirectory, sample).stream().filter(x -> reporterData().panelGeneModel().panel().contains(x.gene())).collect(Collectors.toList());
    LOGGER.info("  " + purpleCopyNumbers.size() + " purple copy number regions loaded for sample " + sample);
    LOGGER.info(" Analyzing purple somatic copy numbers...");
    final PurpleAnalysis purpleAnalysis = ImmutablePurpleAnalysis.builder().gender(context.gender()).status(context.status()).fittedPurity(purity).fittedScorePurity(purityScore).copyNumbers(purpleCopyNumbers).panelGeneCopyNumbers(panelGeneCopyNumbers).build();
    final Path structuralVariantVCF = PatientReporterHelper.findStructuralVariantVCF(runDirectory);
    LOGGER.info(" Loading structural variants...");
    final List<StructuralVariant> structuralVariants = StructuralVariantFileLoader.fromFile(structuralVariantVCF.toString(), true);
    LOGGER.info(" Enriching structural variants with purple data.");
    final List<EnrichedStructuralVariant> enrichedStructuralVariants = purpleAnalysis.enrichStructuralVariants(structuralVariants);
    LOGGER.info(" Analysing structural variants...");
    final StructuralVariantAnalysis structuralVariantAnalysis = structuralVariantAnalyzer().run(enrichedStructuralVariants, false);
    return ImmutableGenomeAnalysis.of(sample, variantAnalysis, purpleAnalysis, structuralVariantAnalysis);
}