src/toil_lib/tools/variant_manipulation.py
def gatk_combine_variants(job, vcfs, ref_fasta, ref_fai, ref_dict, merge_option='UNIQUIFY'):
    """
    Merges VCF files using GATK CombineVariants

    :param JobFunctionWrappingJob job: Toil Job instance
    :param dict vcfs: Dictionary of VCF FileStoreIDs {sample identifier: FileStoreID}
    :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 str merge_option: Value for --genotypemergeoption flag (Default: 'UNIQUIFY')
                            'UNIQUIFY': Multiple variants at a single site are merged into a
                                        single variant record.
                            'UNSORTED': Used to merge VCFs from the same sample
    :return: FileStoreID for merged VCF file
    :rtype: str
    """
    job.fileStore.logToMaster('Running GATK CombineVariants')

    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict}
    inputs.update(vcfs)

    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', 'CombineVariants',
               '-R', '/data/genome.fa',
               '-o', '/data/merged.vcf',
               '--genotypemergeoption', merge_option]

    for uuid, vcf_id in vcfs.iteritems():
        command.extend(['--variant', os.path.join('/data', uuid)])

    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, 'merged.vcf'))
def gatk_combine_variants(job, vcfs, ref_fasta, ref_fai, ref_dict, merge_option='UNIQUIFY'):
    """
    Merges VCF files using GATK CombineVariants

    :param JobFunctionWrappingJob job: Toil Job instance
    :param dict vcfs: Dictionary of VCF FileStoreIDs {sample identifier: FileStoreID}
    :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 str merge_option: Value for --genotypemergeoption flag (Default: 'UNIQUIFY')
                            'UNIQUIFY': Multiple variants at a single site are merged into a
                                        single variant record.
                            'UNSORTED': Used to merge VCFs from the same sample
    :return: FileStoreID for merged VCF file
    :rtype: str
    """
    job.fileStore.logToMaster('Running GATK CombineVariants')

    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict}
    inputs.update(vcfs)

    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', 'CombineVariants',
               '-R', '/data/genome.fa',
               '-o', '/data/merged.vcf',
               '--genotypemergeoption', merge_option]

    for uuid, vcf_id in vcfs.iteritems():
        command.extend(['--variant', os.path.join('/data', uuid)])

    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, 'merged.vcf'))
Merges VCF files using GATK CombineVariants

    :param JobFunctionWrappingJob job: Toil Job instance
    :param dict vcfs: Dictionary of VCF FileStoreIDs {sample identifier: FileStoreID}
    :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 str merge_option: Value for --genotypemergeoption flag (Default: 'UNIQUIFY')
                            'UNIQUIFY': Multiple variants at a single site are merged into a
                                        single variant record.
                            'UNSORTED': Used to merge VCFs from the same sample
    :return: FileStoreID for merged VCF file
    :rtype: str