Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary

    :param bam_file: (str) path of the bam_file
    :param data: (list) list containing the all the dictionary
                     for this sample
    :param out_dir: (str) path of the output

    :returns: (string) output normalized vcf file

def run(bam_file, data, out_dir):
    """ Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary

    :param bam_file: (str) path of the bam_file
    :param data: (list) list containing the all the dictionary
                     for this sample
    :param out_dir: (str) path of the output

    :returns: (string) output normalized vcf file
    """
    qsig = config_utils.get_program("qsignature", data["config"])
    res_qsig = config_utils.get_resources("qsignature", data["config"])
    jvm_opts = " ".join(res_qsig.get("jvm_opts", ["-Xms750m", "-Xmx8g"]))
    if not qsig:
        logger.info("There is no qsignature tool. Skipping...")
        return None

    position = dd.get_qsig_file(data)
    mixup_check = dd.get_mixup_check(data)
    if mixup_check and mixup_check.startswith("qsignature"):
        utils.safe_makedir(out_dir)
        if not position:
            logger.info("There is no qsignature for this species: %s"
                        % tz.get_in(['genome_build'], data))
            return None
        if mixup_check == "qsignature_full":
            down_bam = bam_file
        else:
            down_bam = _slice_bam_chr21(bam_file, data)
            position = _slice_vcf_chr21(position, out_dir)

        out_name = os.path.basename(down_bam).replace("bam", "qsig.vcf")
        out_file = os.path.join(out_dir, out_name)
        log_file = os.path.join(out_dir, "qsig.log")
        cores = dd.get_cores(data)
        base_cmd = ("{qsig} {jvm_opts} "
                    "org.qcmg.sig.SignatureGenerator "
                    "--noOfThreads {cores} "
                    "-log {log_file} -i {position} "
                    "-i {down_bam} ")
        if not os.path.exists(out_file):
            file_qsign_out = "{0}.qsig.vcf".format(down_bam)
            do.run(base_cmd.format(**locals()), "qsignature vcf generation: %s" % dd.get_sample_name(data))
            if os.path.exists(file_qsign_out):
                with file_transaction(data, out_file) as file_txt_out:
                    shutil.move(file_qsign_out, file_txt_out)
            else:
                raise IOError("File doesn't exist %s" % file_qsign_out)
        return out_file
    return None