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

Example 1 with BayesianHetPulldownCalculator

use of org.broadinstitute.hellbender.tools.exome.pulldown.BayesianHetPulldownCalculator in project gatk 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);
}

Example 2 with BayesianHetPulldownCalculator

use of org.broadinstitute.hellbender.tools.exome.pulldown.BayesianHetPulldownCalculator 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 3 with BayesianHetPulldownCalculator

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

the class GetBayesianHetCoverage method runMatchedNormalTumor.

/**
     * The matched norrmal-tumor workflow
     */
private void runMatchedNormalTumor() {
    final BayesianHetPulldownCalculator normalHetPulldownCalculator, tumorHetPulldownCalculator;
    final Pulldown normalHetPulldown, tumorHetPulldown;
    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);
    tumorHetPulldownCalculator = new BayesianHetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), normalHetPulldown.getIntervals(), minimumMappingQuality, minimumBaseQuality, readDepthThreshold, VALIDATION_STRINGENCY, errorProbabilityAdjustmentFactor, new BalancedHeterozygousPileupPriorModel());
    logger.info("Calculating the Het pulldown from the tumor BAM file on Hets detected in the normal BAM file...");
    tumorHetPulldown = tumorHetPulldownCalculator.getTumorHetPulldownFromNormalPulldown(tumorBamFile, normalHetPulldown);
    logger.info("Writing Het pulldown from tumor reads to " + tumorHetOutputFile.toString());
    tumorHetPulldown.write(tumorHetOutputFile, AllelicCountTableColumn.AllelicCountTableVerbosity.INTERMEDIATE);
}

Example 4 with BayesianHetPulldownCalculator

use of org.broadinstitute.hellbender.tools.exome.pulldown.BayesianHetPulldownCalculator 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);
}

Example 5 with BayesianHetPulldownCalculator

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

the class GetBayesianHetCoverage method runMatchedNormalTumor.

/**
     * The matched norrmal-tumor workflow
     */
private void runMatchedNormalTumor() {
    final BayesianHetPulldownCalculator normalHetPulldownCalculator, tumorHetPulldownCalculator;
    final Pulldown normalHetPulldown, tumorHetPulldown;
    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);
    tumorHetPulldownCalculator = new BayesianHetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), normalHetPulldown.getIntervals(), minimumMappingQuality, minimumBaseQuality, readDepthThreshold, VALIDATION_STRINGENCY, errorProbabilityAdjustmentFactor, new BalancedHeterozygousPileupPriorModel());
    logger.info("Calculating the Het pulldown from the tumor BAM file on Hets detected in the normal BAM file...");
    tumorHetPulldown = tumorHetPulldownCalculator.getTumorHetPulldownFromNormalPulldown(tumorBamFile, normalHetPulldown);
    logger.info("Writing Het pulldown from tumor reads to " + tumorHetOutputFile.toString());
    tumorHetPulldown.write(tumorHetOutputFile, AllelicCountTableColumn.AllelicCountTableVerbosity.INTERMEDIATE);
}