src/toil_lib/tools/preprocessing.py
def run_base_recalibration(job, bam, bai, ref, ref_dict, fai, dbsnp, mills, unsafe=False):
    """
    Creates recalibration table for Base Quality Score Recalibration

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str bam: FileStoreID for BAM file
    :param str bai: FileStoreID for BAM index file
    :param str ref: FileStoreID for reference genome fasta file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :param str fai: FileStoreID for reference genome fasta index file
    :param str dbsnp: FileStoreID for dbSNP VCF file
    :param str mills: FileStoreID for Mills VCF file
    :param bool unsafe: If True, runs GATK in UNSAFE mode: "-U ALLOW_SEQ_DICT_INCOMPATIBILITY"
    :return: FileStoreID for the recalibration table file
    :rtype: str
    """
    inputs = {'ref.fasta': ref,
              'ref.fasta.fai': fai,
              'ref.dict': ref_dict,
              'input.bam': bam,
              'input.bai': bai,
              'dbsnp.vcf': dbsnp,
              'mills.vcf': mills}

    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))

    # Call: GATK -- BaseRecalibrator
    parameters = ['-T', 'BaseRecalibrator',
                  '-nct', str(int(job.cores)),
                  '-R', '/data/ref.fasta',
                  '-I', '/data/input.bam',
                  # Recommended known sites:
                  # https://software.broadinstitute.org/gatk/guide/article?id=1247
                  '-knownSites', '/data/dbsnp.vcf',
                  '-knownSites', '/data/mills.vcf',
                  '-o', '/data/recal_data.table']

    if unsafe:
        parameters.extend(['-U', 'ALLOW_SEQ_DICT_INCOMPATIBILITY'])

    # Set TMPDIR to /data to prevent writing temporary files to /tmp
    docker_parameters = ['--rm',
                         '--log-driver', 'none',
                         '-e', 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory),
                         '-v', '{}:/data'.format(work_dir)]
    start_time = time.time()
    dockerCall(job=job, tool='quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2',
               workDir=work_dir,
               parameters=parameters,
               dockerParameters=docker_parameters)
    end_time = time.time()
    _log_runtime(job, start_time, end_time, "GATK3 BaseRecalibrator")

    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'recal_data.table'))
def run_base_recalibration(job, bam, bai, ref, ref_dict, fai, dbsnp, mills, unsafe=False):
    inputs = {'ref.fasta': ref,
              'ref.fasta.fai': fai,
              'ref.dict': ref_dict,
              'input.bam': bam,
              'input.bai': bai,
              'dbsnp.vcf': dbsnp,
              'mills.vcf': mills}

    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))

    # Call: GATK -- BaseRecalibrator
    parameters = ['-T', 'BaseRecalibrator',
                  '-nct', str(int(job.cores)),
                  '-R', '/data/ref.fasta',
                  '-I', '/data/input.bam',
                  # Recommended known sites:
                  # https://software.broadinstitute.org/gatk/guide/article?id=1247
                  '-knownSites', '/data/dbsnp.vcf',
                  '-knownSites', '/data/mills.vcf',
                  '-o', '/data/recal_data.table']

    if unsafe:
        parameters.extend(['-U', 'ALLOW_SEQ_DICT_INCOMPATIBILITY'])

    # Set TMPDIR to /data to prevent writing temporary files to /tmp
    docker_parameters = ['--rm',
                         '--log-driver', 'none',
                         '-e', 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory),
                         '-v', '{}:/data'.format(work_dir)]
    start_time = time.time()
    dockerCall(job=job, tool='quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2',
               workDir=work_dir,
               parameters=parameters,
               dockerParameters=docker_parameters)
    end_time = time.time()
    _log_runtime(job, start_time, end_time, "GATK3 BaseRecalibrator")

    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'recal_data.table'))
def run_base_recalibration ( job , bam , bai , ref , ref_dict , fai , dbsnp , mills , unsafe = False ) : inputs = { 'ref.fasta' : ref , 'ref.fasta.fai' : fai , 'ref.dict' : ref_dict , 'input.bam' : bam , 'input.bai' : bai , 'dbsnp.vcf' : dbsnp , 'mills.vcf' : mills } 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 ) ) # Call: GATK -- BaseRecalibrator parameters = [ '-T' , 'BaseRecalibrator' , '-nct' , str ( int ( job . cores ) ) , '-R' , '/data/ref.fasta' , '-I' , '/data/input.bam' , # Recommended known sites: # https://software.broadinstitute.org/gatk/guide/article?id=1247 '-knownSites' , '/data/dbsnp.vcf' , '-knownSites' , '/data/mills.vcf' , '-o' , '/data/recal_data.table' ] if unsafe : parameters . extend ( [ '-U' , 'ALLOW_SEQ_DICT_INCOMPATIBILITY' ] ) # Set TMPDIR to /data to prevent writing temporary files to /tmp docker_parameters = [ '--rm' , '--log-driver' , 'none' , '-e' , 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}' . format ( job . memory ) , '-v' , '{}:/data' . format ( work_dir ) ] start_time = time . time ( ) dockerCall ( job = job , tool = 'quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2' , workDir = work_dir , parameters = parameters , dockerParameters = docker_parameters ) end_time = time . time ( ) _log_runtime ( job , start_time , end_time , "GATK3 BaseRecalibrator" ) return job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'recal_data.table' ) )
Creates recalibration table for Base Quality Score Recalibration

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str bam: FileStoreID for BAM file
    :param str bai: FileStoreID for BAM index file
    :param str ref: FileStoreID for reference genome fasta file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :param str fai: FileStoreID for reference genome fasta index file
    :param str dbsnp: FileStoreID for dbSNP VCF file
    :param str mills: FileStoreID for Mills VCF file
    :param bool unsafe: If True, runs GATK in UNSAFE mode: "-U ALLOW_SEQ_DICT_INCOMPATIBILITY"
    :return: FileStoreID for the recalibration table file
    :rtype: str
Creates recalibration table for Base Quality Score Recalibration