use of org.broadinstitute.hellbender.tools.exome.pulldown.HetPulldownCalculator in project gatk by broadinstitute.
the class GetHetCoverage method doWork.
@Override
protected Object doWork() {
//if tumor arguments are missing, throw exception (and do not even get normal pulldown)
final boolean doTumorPulldown;
if (tumorHetOutputFile != null && tumorBAMFile != null) {
doTumorPulldown = true;
} else if ((tumorHetOutputFile == null) != (tumorBAMFile == null)) {
throw new CommandLineException("Must specify both BAM and output files for tumor pulldown.");
} else {
doTumorPulldown = false;
}
final HetPulldownCalculator hetPulldown = new HetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), snpFile, minimumMappingQuality, minimumBaseQuality, VALIDATION_STRINGENCY);
logger.info("Getting normal het pulldown...");
final Pulldown normalHetPulldown = hetPulldown.getNormal(normalBAMFile, pvalThreshold, minimumRawReads);
normalHetPulldown.write(normalHetOutputFile, AllelicCountTableVerbosity.BASIC);
logger.info("Normal het pulldown written to " + normalHetOutputFile.toString());
if (doTumorPulldown) {
final IntervalList normalHetIntervals = normalHetPulldown.getIntervals();
logger.info("Getting tumor het pulldown...");
final Pulldown tumorHetPulldown = hetPulldown.getTumor(tumorBAMFile, normalHetIntervals, minimumRawReads);
tumorHetPulldown.write(tumorHetOutputFile, AllelicCountTableVerbosity.BASIC);
logger.info("Tumor het pulldown written to " + tumorHetOutputFile.toString());
}
return "SUCCESS";
}
use of org.broadinstitute.hellbender.tools.exome.pulldown.HetPulldownCalculator in project gatk-protected by broadinstitute.
the class GetHetCoverage method doWork.
@Override
protected Object doWork() {
//if tumor arguments are missing, throw exception (and do not even get normal pulldown)
final boolean doTumorPulldown;
if (tumorHetOutputFile != null && tumorBAMFile != null) {
doTumorPulldown = true;
} else if ((tumorHetOutputFile == null) != (tumorBAMFile == null)) {
throw new CommandLineException("Must specify both BAM and output files for tumor pulldown.");
} else {
doTumorPulldown = false;
}
final HetPulldownCalculator hetPulldown = new HetPulldownCalculator(REFERENCE_ARGUMENTS.getReferenceFile(), snpFile, minimumMappingQuality, minimumBaseQuality, VALIDATION_STRINGENCY);
logger.info("Getting normal het pulldown...");
final Pulldown normalHetPulldown = hetPulldown.getNormal(normalBAMFile, pvalThreshold, minimumRawReads);
normalHetPulldown.write(normalHetOutputFile, AllelicCountTableVerbosity.BASIC);
logger.info("Normal het pulldown written to " + normalHetOutputFile.toString());
if (doTumorPulldown) {
final IntervalList normalHetIntervals = normalHetPulldown.getIntervals();
logger.info("Getting tumor het pulldown...");
final Pulldown tumorHetPulldown = hetPulldown.getTumor(tumorBAMFile, normalHetIntervals, minimumRawReads);
tumorHetPulldown.write(tumorHetOutputFile, AllelicCountTableVerbosity.BASIC);
logger.info("Tumor het pulldown written to " + tumorHetOutputFile.toString());
}
return "SUCCESS";
}
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