Process the MuTect vcf for accepted calls.

    :param toil.fileStore.FileID mutect_vcf: fsID for a MuTect generated chromosome vcf
    :param str work_dir: Working directory
    :param dict univ_options: Dict of universal options used by almost all tools
    :return: Path to the processed vcf
    :rtype: str

def process_mutect_vcf(job, mutect_vcf, work_dir, univ_options):
    """
    Process the MuTect vcf for accepted calls.

    :param toil.fileStore.FileID mutect_vcf: fsID for a MuTect generated chromosome vcf
    :param str work_dir: Working directory
    :param dict univ_options: Dict of universal options used by almost all tools
    :return: Path to the processed vcf
    :rtype: str
    """
    mutect_vcf = job.fileStore.readGlobalFile(mutect_vcf)

    with open(mutect_vcf, 'r') as infile, open(mutect_vcf + 'mutect_parsed.tmp', 'w') as outfile:
        for line in infile:
            line = line.strip()
            if line.startswith('#'):
                print(line, file=outfile)
                continue
            line = line.split('\t')
            if line[6] != 'REJECT':
                print('\t'.join(line), file=outfile)
    return outfile.name