src/toil_lib/tools/variant_manipulation.py
def gatk_apply_variant_recalibration(job,
                                     mode,
                                     vcf,
                                     recal_table, tranches,
                                     ref_fasta, ref_fai, ref_dict,
                                     ts_filter_level=99.0,
                                     unsafe_mode=False):
    """
    Applies variant quality score recalibration to VCF file using GATK ApplyRecalibration

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str mode: Determines variant recalibration mode (SNP or INDEL)
    :param str vcf: FileStoreID for input VCF file
    :param str recal_table: FileStoreID for recalibration table file
    :param str tranches: FileStoreID for tranches file
    :param str ref_fasta: FileStoreID for reference genome fasta
    :param str ref_fai: FileStoreID for reference genome index file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :param float ts_filter_level: Sensitivity expressed as a percentage, default is 99.0
    :param bool unsafe_mode: If True, runs gatk UNSAFE mode: "-U ALLOW_SEQ_DICT_INCOMPATIBILITY"
    :return: FileStoreID for recalibrated VCF file
    :rtype: str
    """
    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict,
              'input.vcf': vcf,
              'recal': recal_table,
              'tranches': tranches}

    work_dir = job.fileStore.getLocalTempDir()
    for name, file_store_id in inputs.iteritems():
        job.fileStore.readGlobalFile(file_store_id, os.path.join(work_dir, name))

    mode = mode.upper()

    # GATK recommended parameters:
    # https://software.broadinstitute.org/gatk/documentation/article?id=2805
    command = ['-T', 'ApplyRecalibration',
               '-mode', mode,
               '-R', 'genome.fa',
               '-input', 'input.vcf',
               '-o', 'vqsr.vcf',
               '-ts_filter_level', str(ts_filter_level),
               '-recalFile', 'recal',
               '-tranchesFile', 'tranches']

    if unsafe_mode:
        command.extend(['-U', 'ALLOW_SEQ_DICT_INCOMPATIBILITY'])

    job.fileStore.logToMaster('Running GATK ApplyRecalibration on {mode}s '
                              'with a sensitivity of {sensitivity}%'.format(mode=mode,
                                                                            sensitivity=ts_filter_level))
    docker_parameters = ['--rm', 'log-driver', 'none',
                         '-e', 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory)]
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2',
               dockerParameters=docker_parameters)

    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'vqsr.vcf'))
def gatk_apply_variant_recalibration(job,
                                     mode,
                                     vcf,
                                     recal_table, tranches,
                                     ref_fasta, ref_fai, ref_dict,
                                     ts_filter_level=99.0,
                                     unsafe_mode=False):
    """
    Applies variant quality score recalibration to VCF file using GATK ApplyRecalibration

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str mode: Determines variant recalibration mode (SNP or INDEL)
    :param str vcf: FileStoreID for input VCF file
    :param str recal_table: FileStoreID for recalibration table file
    :param str tranches: FileStoreID for tranches file
    :param str ref_fasta: FileStoreID for reference genome fasta
    :param str ref_fai: FileStoreID for reference genome index file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :param float ts_filter_level: Sensitivity expressed as a percentage, default is 99.0
    :param bool unsafe_mode: If True, runs gatk UNSAFE mode: "-U ALLOW_SEQ_DICT_INCOMPATIBILITY"
    :return: FileStoreID for recalibrated VCF file
    :rtype: str
    """
    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict,
              'input.vcf': vcf,
              'recal': recal_table,
              'tranches': tranches}

    work_dir = job.fileStore.getLocalTempDir()
    for name, file_store_id in inputs.iteritems():
        job.fileStore.readGlobalFile(file_store_id, os.path.join(work_dir, name))

    mode = mode.upper()

    # GATK recommended parameters:
    # https://software.broadinstitute.org/gatk/documentation/article?id=2805
    command = ['-T', 'ApplyRecalibration',
               '-mode', mode,
               '-R', 'genome.fa',
               '-input', 'input.vcf',
               '-o', 'vqsr.vcf',
               '-ts_filter_level', str(ts_filter_level),
               '-recalFile', 'recal',
               '-tranchesFile', 'tranches']

    if unsafe_mode:
        command.extend(['-U', 'ALLOW_SEQ_DICT_INCOMPATIBILITY'])

    job.fileStore.logToMaster('Running GATK ApplyRecalibration on {mode}s '
                              'with a sensitivity of {sensitivity}%'.format(mode=mode,
                                                                            sensitivity=ts_filter_level))
    docker_parameters = ['--rm', 'log-driver', 'none',
                         '-e', 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory)]
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2',
               dockerParameters=docker_parameters)

    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'vqsr.vcf'))
Applies variant quality score recalibration to VCF file using GATK ApplyRecalibration

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str mode: Determines variant recalibration mode (SNP or INDEL)
    :param str vcf: FileStoreID for input VCF file
    :param str recal_table: FileStoreID for recalibration table file
    :param str tranches: FileStoreID for tranches file
    :param str ref_fasta: FileStoreID for reference genome fasta
    :param str ref_fai: FileStoreID for reference genome index file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :param float ts_filter_level: Sensitivity expressed as a percentage, default is 99.0
    :param bool unsafe_mode: If True, runs gatk UNSAFE mode: "-U ALLOW_SEQ_DICT_INCOMPATIBILITY"
    :return: FileStoreID for recalibrated VCF file
    :rtype: str