def combine_cosmic(fnames, ref_file):
    out_file = "cosmic-%s-GRCh37.vcf" % VERSION
    if not os.path.exists(out_file):
        cmd = ["gatk-framework", "-T", "CombineVariants", "-R", ref_file, "--out", out_file,
               "--suppressCommandLineHeader", "--setKey", "null"]
        for v in fnames:
            cmd += ["--variant", v]
        subprocess.check_call(cmd)
    return out_file
dataset/ETHPy150Open chapmanb/cloudbiolinux/utils/prepare_cosmic.py/combine_cosmic/original