src/toil_lib/tools/variant_manipulation.py
def gatk_variant_filtration(job, vcf_id, filter_name, filter_expression, ref_fasta, ref_fai, ref_dict):
    """
    Filters VCF file using GATK VariantFiltration. Fixes extra pair of quotation marks in VCF header that
    may interfere with other VCF tools.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str vcf_id: FileStoreID for input VCF file
    :param str filter_name: Name of filter for VCF header
    :param str filter_expression: JEXL filter expression
    :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
    :return: FileStoreID for filtered VCF file
    :rtype: str
    """
    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict,
              'input.vcf': vcf_id}

    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))

    command = ['-T', 'VariantFiltration',
               '-R', 'genome.fa',
               '-V', 'input.vcf',
               '--filterName', filter_name,   # Documents filter name in header
               '--filterExpression', filter_expression,
               '-o', 'filtered_variants.vcf']

    job.fileStore.logToMaster('Running GATK VariantFiltration using {name}: '
                              '{expression}'.format(name=filter_name, expression=filter_expression))

    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)

    # Remove extra quotation marks around filter expression.
    malformed_header = os.path.join(work_dir, 'filtered_variants.vcf')
    fixed_header = os.path.join(work_dir, 'fixed_header.vcf')
    filter_regex = re.escape('"%s"' % filter_expression)
    with open(malformed_header, 'r') as f, open(fixed_header, 'w') as g:
        for line in f:
            g.write(re.sub(filter_regex, filter_expression, line))

    return job.fileStore.writeGlobalFile(fixed_header)
def gatk_variant_filtration(job, vcf_id, filter_name, filter_expression, ref_fasta, ref_fai, ref_dict):
    """
    Filters VCF file using GATK VariantFiltration. Fixes extra pair of quotation marks in VCF header that
    may interfere with other VCF tools.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str vcf_id: FileStoreID for input VCF file
    :param str filter_name: Name of filter for VCF header
    :param str filter_expression: JEXL filter expression
    :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
    :return: FileStoreID for filtered VCF file
    :rtype: str
    """
    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict,
              'input.vcf': vcf_id}

    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))

    command = ['-T', 'VariantFiltration',
               '-R', 'genome.fa',
               '-V', 'input.vcf',
               '--filterName', filter_name,   # Documents filter name in header
               '--filterExpression', filter_expression,
               '-o', 'filtered_variants.vcf']

    job.fileStore.logToMaster('Running GATK VariantFiltration using {name}: '
                              '{expression}'.format(name=filter_name, expression=filter_expression))

    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)

    # Remove extra quotation marks around filter expression.
    malformed_header = os.path.join(work_dir, 'filtered_variants.vcf')
    fixed_header = os.path.join(work_dir, 'fixed_header.vcf')
    filter_regex = re.escape('"%s"' % filter_expression)
    with open(malformed_header, 'r') as f, open(fixed_header, 'w') as g:
        for line in f:
            g.write(re.sub(filter_regex, filter_expression, line))

    return job.fileStore.writeGlobalFile(fixed_header)
Filters VCF file using GATK VariantFiltration. Fixes extra pair of quotation marks in VCF header that
    may interfere with other VCF tools.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str vcf_id: FileStoreID for input VCF file
    :param str filter_name: Name of filter for VCF header
    :param str filter_expression: JEXL filter expression
    :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
    :return: FileStoreID for filtered VCF file
    :rtype: str