filter paired vcf file with GATK
    :param    tumor: (str) sample name for tumor
    :param    normal: (str) sample name for normal
    :param    out_file: (str) final vcf file
    :param    reference: (str) genome in fasta format
    :param    data: (dict) information from yaml file(items[0])
    :returns: (str) name of final vcf file

def _filter_paired(tumor, normal, out_file, reference, data):
    """filter paired vcf file with GATK
    :param    tumor: (str) sample name for tumor
    :param    normal: (str) sample name for normal
    :param    out_file: (str) final vcf file
    :param    reference: (str) genome in fasta format
    :param    data: (dict) information from yaml file(items[0])
    :returns: (str) name of final vcf file
    """
    in_file = utils.splitext_plus(out_file)[0] + "-tmp.vcf"
    shutil.move(out_file, in_file)
    config = data["config"]
    with file_transaction(data, out_file) as tx_out_file:
        params = ["-T", "SomaticPindelFilter", "-V", in_file, "-o",
                  tx_out_file, "-TID", tumor, "-NID", normal, "-R", reference]
        jvm_opts = broad.get_gatk_opts(config)
        do.run(broad.gatk_cmd("gatk-framework", jvm_opts, params), "Filter pindel variants")
    return out_file