Examples with HeterogeneousHeterozygousPileupPriorModel org.broadinstitute.hellbender.tools.exome.pulldown.HeterogeneousHeterozygousPileupPriorModel used on opensource projects

Example 1 with HeterogeneousHeterozygousPileupPriorModel

use of org.broadinstitute.hellbender.tools.exome.pulldown.HeterogeneousHeterozygousPileupPriorModel in project gatk by broadinstitute.

the class GetBayesianHetCoverage method runTumorOnly.

/**
     * The tumor-only workflow
     */
private void runTumorOnly() {
    final BayesianHetPulldownCalculator tumorHetPulldownCalculator;
    final Pulldown tumorHetPulldown;
    tumorHetPulldownCalculator = new BayesianHetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), IntervalList.fromFile(snpFile), minimumMappingQuality, minimumBaseQuality, readDepthThreshold, VALIDATION_STRINGENCY, errorProbabilityAdjustmentFactor, new HeterogeneousHeterozygousPileupPriorModel(minimumAbnormalFraction, maximumAbnormalFraction, maximumCopyNumber, quadratureOrder));
    logger.info("Calculating the Het pulldown from the tumor BAM file using the HETEROGENEOUS prior...");
    tumorHetPulldown = tumorHetPulldownCalculator.getHetPulldown(tumorBamFile, hetCallingStringency);
    logger.info("Writing Het pulldown from tumor reads to " + tumorHetOutputFile.toString());
    tumorHetPulldown.write(tumorHetOutputFile, AllelicCountTableColumn.AllelicCountTableVerbosity.FULL);
}

Example 2 with HeterogeneousHeterozygousPileupPriorModel

use of org.broadinstitute.hellbender.tools.exome.pulldown.HeterogeneousHeterozygousPileupPriorModel in project gatk-protected by broadinstitute.

the class GetBayesianHetCoverage method runTumorOnly.

/**
     * The tumor-only workflow
     */
private void runTumorOnly() {
    final BayesianHetPulldownCalculator tumorHetPulldownCalculator;
    final Pulldown tumorHetPulldown;
    tumorHetPulldownCalculator = new BayesianHetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), IntervalList.fromFile(snpFile), minimumMappingQuality, minimumBaseQuality, readDepthThreshold, VALIDATION_STRINGENCY, errorProbabilityAdjustmentFactor, new HeterogeneousHeterozygousPileupPriorModel(minimumAbnormalFraction, maximumAbnormalFraction, maximumCopyNumber, quadratureOrder));
    logger.info("Calculating the Het pulldown from the tumor BAM file using the HETEROGENEOUS prior...");
    tumorHetPulldown = tumorHetPulldownCalculator.getHetPulldown(tumorBamFile, hetCallingStringency);
    logger.info("Writing Het pulldown from tumor reads to " + tumorHetOutputFile.toString());
    tumorHetPulldown.write(tumorHetOutputFile, AllelicCountTableColumn.AllelicCountTableVerbosity.FULL);
}