Convenience function to get the vcf from the patient dict

    :param dict patient_dict: dict of patient info
    :return: The vcf
    :rtype: toil.fileStore.FileID

def get_patient_vcf(job, patient_dict):
    """
    Convenience function to get the vcf from the patient dict

    :param dict patient_dict: dict of patient info
    :return: The vcf
    :rtype: toil.fileStore.FileID
    """
    temp = job.fileStore.readGlobalFile(patient_dict['mutation_vcf'],
                                        os.path.join(os.getcwd(), 'temp.gz'))
    if is_gzipfile(temp):
        outfile = job.fileStore.writeGlobalFile(gunzip(temp))
        job.fileStore.deleteGlobalFile(patient_dict['mutation_vcf'])
    else:
        outfile = patient_dict['mutation_vcf']
    return outfile