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

Example 6 with BayesianHetPulldownCalculator

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

the class GetBayesianHetCoverage method runNormalOnly.

/**
     * The normal-only workflow
     */
private void runNormalOnly() {
    final BayesianHetPulldownCalculator normalHetPulldownCalculator;
    final Pulldown normalHetPulldown;
    normalHetPulldownCalculator = new BayesianHetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), IntervalList.fromFile(snpFile), minimumMappingQuality, minimumBaseQuality, readDepthThreshold, VALIDATION_STRINGENCY, errorProbabilityAdjustmentFactor, new BalancedHeterozygousPileupPriorModel());
    logger.info("Calculating the Het pulldown from the normal BAM file using the BALANCED prior...");
    normalHetPulldown = normalHetPulldownCalculator.getHetPulldown(normalBamFile, hetCallingStringency);
    logger.info("Writing Het pulldown from normal reads to " + normalHetOutputFile.toString());
    normalHetPulldown.write(normalHetOutputFile, AllelicCountTableColumn.AllelicCountTableVerbosity.FULL);
}