Examples of org.broadinstitute.gatk.utils.MendelianViolation

org.broadinstitute.gatk.utils.MendelianViolation
User: carneiro / lfran Date: 3/9/11 Time: 12:38 PM Class for the identification and tracking of mendelian violation. It can be used in 2 distinct ways: - Either using an instance of the MendelianViolation class to track mendelian violations for each of the families while walking over the variants - Or using the static methods to directly get information about mendelian violation in a family at a given locus

                                        final VariantContext vc,
                                        final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
        if ( mendelianViolation == null ) {
            trios = ((Walker) walker).getSampleDB().getTrios();
            if ( trios.size() > 0 ) {
                mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
            }
            else {
                throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator, and must be provided a valid PED file (-ped) from the command line.");
            }
        }

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                                        final VariantContext vc,
                                        final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
        if ( mendelianViolation == null ) {
            trios = ((Walker) walker).getSampleDB().getTrios();
            if ( trios.size() > 0 ) {
                mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
            }
            else {
                throw new UserException("Possible de novos annotation can only be used from the Variant Annotator, and must be provided a valid PED file (-ped) from the command line.");
            }
        }

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        CONCORDANCE_ONLY = concordanceTrack.isBound();
        if (CONCORDANCE_ONLY) logger.info("Selecting only variants concordant with the track: " + concordanceTrack.getName());


        if (MENDELIAN_VIOLATIONS) {
            mv = new MendelianViolation(MENDELIAN_VIOLATION_QUAL_THRESHOLD,false,true);
        }


        SELECT_RANDOM_FRACTION = fractionRandom > 0;
        if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track");

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    MendelianViolation mv;
    Map<String,Set<Sample>> families;


    public void initialize(VariantEval walker) {
        super.initialize(walker);
        mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false);
        families = walker.getSampleDB().getFamilies();
    }

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Related Classes of org.broadinstitute.gatk.utils.MendelianViolation

htsjdk.variant.variantcontext.Genotype

org.broadinstitute.gatk.engine.samples.Sample

org.broadinstitute.gatk.tools.walkers.annotator.MVLikelihoodRatio

org.broadinstitute.gatk.tools.walkers.annotator.PossibleDeNovo

org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator

org.broadinstitute.gatk.tools.walkers.variantutils.SelectVariants

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