Examples with AllelicCalls org.broadinstitute.hellbender.tools.exome.conversion.allelicbalancecaller.AllelicCalls used on opensource projects

Example 1 with AllelicCalls

use of org.broadinstitute.hellbender.tools.exome.conversion.allelicbalancecaller.AllelicCalls in project gatk by broadinstitute.

the class ConvertACNVResults method runPipeline.

@Override
protected void runPipeline(final JavaSparkContext ctx) {
    final String originalLogLevel = (ctx.getLocalProperty("logLevel") != null) ? ctx.getLocalProperty("logLevel") : "INFO";
    ctx.setLogLevel("WARN");
    final CNLOHCaller cnlohCaller = new CNLOHCaller();
    cnlohCaller.setRhoThreshold(rhoThreshold);
    final List<ACNVModeledSegment> segments = SegmentUtils.readACNVModeledSegmentFile(new File(segmentsFile));
    String sampleName = determineSampleName(new File(segmentsFile));
    // Create the outputdir
    try {
        FileUtils.forceMkdir(outputDir);
    } catch (final IOException ioe) {
        throw new UserException("Cannot create " + outputDir + ".  Does a file (not directory) exist with the same name?  Do you have access to create?", ioe);
    }
    final Genome genome = new Genome(targetCoveragesFile, snpCountsFile);
    // Make the calls
    logger.info("Making the balanced-segment (and CNLoH) calls...");
    final List<AllelicCalls> calls = cnlohCaller.makeCalls(segments, numIterations, ctx);
    // Write updated ACNV file with calls
    logger.info("Writing updated ACNV file with calls ...");
    final File finalACNVModeledSegmentsFile = new File(outputDir, getSegmentsBaseFilename() + "." + BALANCED_SEG_FILE_TAG + ".seg");
    SegmentUtils.writeCnLoHACNVModeledSegmentFile(finalACNVModeledSegmentsFile, calls, genome);
    // write file for GATK CNV formatted seg file
    logger.info("Writing file with same output format as GATK CNV...");
    final File finalModeledSegmentsFileAsGatkCNV = new File(outputDir, getSegmentsBaseFilename() + "." + GATK_SEG_FILE_TAG + ".seg");
    SegmentUtils.writeModeledSegmentFile(finalModeledSegmentsFileAsGatkCNV, ACNVModeledSegmentConversionUtils.convertACNVModeledSegmentsToModeledSegments(segments, genome), sampleName);
    //write file for ACS-compatible output to help Broad CGA
    logger.info("Writing file with same output format as Broad CGA Allelic CapSeg ...");
    final File finalACSModeledSegmentsFile = new File(outputDir, getSegmentsBaseFilename() + "." + CGA_ACS_SEG_FILE_TAG + ".seg");
    ACSModeledSegmentUtils.writeACNVModeledSegmentFileAsAllelicCapSegFile(finalACSModeledSegmentsFile, calls, genome);
    //write files for TITAN-compatible output to help Broad CGA
    logger.info("Writing het file with input format for TITAN ...");
    final File finalTitanHetFile = new File(outputDir, getSegmentsBaseFilename() + "." + TITAN_HET_FILE_TAG + ".tsv");
    TitanFileConverter.convertHetPulldownToTitanHetFile(snpCountsFile, finalTitanHetFile);
    logger.info("Writing tangent-normalized target CR estimates with input format for TITAN ...");
    final File finalTitanTNFile = new File(outputDir, getSegmentsBaseFilename() + "." + TITAN_TN_FILE_TAG + ".tsv");
    TitanFileConverter.convertCRToTitanCovFile(targetCoveragesFile, finalTitanTNFile);
    ctx.setLogLevel(originalLogLevel);
    logger.info("SUCCESS: CNLoH and splits called for sample " + sampleName + ".");
}

Example 2 with AllelicCalls

use of org.broadinstitute.hellbender.tools.exome.conversion.allelicbalancecaller.AllelicCalls in project gatk-protected by broadinstitute.

the class ConvertACNVResults method runPipeline.

@Override
protected void runPipeline(final JavaSparkContext ctx) {
    final String originalLogLevel = (ctx.getLocalProperty("logLevel") != null) ? ctx.getLocalProperty("logLevel") : "INFO";
    ctx.setLogLevel("WARN");
    final CNLOHCaller cnlohCaller = new CNLOHCaller();
    cnlohCaller.setRhoThreshold(rhoThreshold);
    final List<ACNVModeledSegment> segments = SegmentUtils.readACNVModeledSegmentFile(new File(segmentsFile));
    String sampleName = determineSampleName(new File(segmentsFile));
    // Create the outputdir
    try {
        FileUtils.forceMkdir(outputDir);
    } catch (final IOException ioe) {
        throw new UserException("Cannot create " + outputDir + ".  Does a file (not directory) exist with the same name?  Do you have access to create?", ioe);
    }
    final Genome genome = new Genome(targetCoveragesFile, snpCountsFile);
    // Make the calls
    logger.info("Making the balanced-segment (and CNLoH) calls...");
    final List<AllelicCalls> calls = cnlohCaller.makeCalls(segments, numIterations, ctx);
    // Write updated ACNV file with calls
    logger.info("Writing updated ACNV file with calls ...");
    final File finalACNVModeledSegmentsFile = new File(outputDir, getSegmentsBaseFilename() + "." + BALANCED_SEG_FILE_TAG + ".seg");
    SegmentUtils.writeCnLoHACNVModeledSegmentFile(finalACNVModeledSegmentsFile, calls, genome);
    // write file for GATK CNV formatted seg file
    logger.info("Writing file with same output format as GATK CNV...");
    final File finalModeledSegmentsFileAsGatkCNV = new File(outputDir, getSegmentsBaseFilename() + "." + GATK_SEG_FILE_TAG + ".seg");
    SegmentUtils.writeModeledSegmentFile(finalModeledSegmentsFileAsGatkCNV, ACNVModeledSegmentConversionUtils.convertACNVModeledSegmentsToModeledSegments(segments, genome), sampleName);
    //write file for ACS-compatible output to help Broad CGA
    logger.info("Writing file with same output format as Broad CGA Allelic CapSeg ...");
    final File finalACSModeledSegmentsFile = new File(outputDir, getSegmentsBaseFilename() + "." + CGA_ACS_SEG_FILE_TAG + ".seg");
    ACSModeledSegmentUtils.writeACNVModeledSegmentFileAsAllelicCapSegFile(finalACSModeledSegmentsFile, calls, genome);
    //write files for TITAN-compatible output to help Broad CGA
    logger.info("Writing het file with input format for TITAN ...");
    final File finalTitanHetFile = new File(outputDir, getSegmentsBaseFilename() + "." + TITAN_HET_FILE_TAG + ".tsv");
    TitanFileConverter.convertHetPulldownToTitanHetFile(snpCountsFile, finalTitanHetFile);
    logger.info("Writing tangent-normalized target CR estimates with input format for TITAN ...");
    final File finalTitanTNFile = new File(outputDir, getSegmentsBaseFilename() + "." + TITAN_TN_FILE_TAG + ".tsv");
    TitanFileConverter.convertCRToTitanCovFile(targetCoveragesFile, finalTitanTNFile);
    ctx.setLogLevel(originalLogLevel);
    logger.info("SUCCESS: CNLoH and splits called for sample " + sampleName + ".");
}