use pindel2vcf to create vcf file from pindel format
    :param root_file: (str) prefix for pindel
    :param out_file: (str) final vcf file
    :param reference (str) genome in fasta format
    :param items: (dics) information fro yaml file
    :param paired: (tupple) bam files and name of tumor/normal samples
    :returns: (str) final vcf file

def _create_vcf(root_file, out_file, reference, items, paired=None):
    """use pindel2vcf to create vcf file from pindel format
    :param root_file: (str) prefix for pindel
    :param out_file: (str) final vcf file
    :param reference (str) genome in fasta format
    :param items: (dics) information fro yaml file
    :param paired: (tupple) bam files and name of tumor/normal samples
    :returns: (str) final vcf file
    """
    config = items[0]["config"]
    name_ref = items[0]["genome_build"]
    date = time.strftime("%Y%m%d")
    if not utils.file_exists(out_file):
        pindel2vcf = config_utils.get_program("pindel2vcf", config)
        vcf_file = out_file.replace(".gz", "")
        with file_transaction(items[0], vcf_file) as tx_out_file:
            cmd = ("{pindel2vcf} --gatk_compatible -P {root_file} -r {reference} -R {name_ref} "
                   "-d {date} -v {tx_out_file} --compact_output_limit 15")
            do.run(cmd.format(**locals()), "Converting to vcf", {})
            if paired.normal_name:
                _filter_paired(paired.tumor_name, paired.normal_name,
                               tx_out_file, reference, items[0])
        out_file = bgzip_and_index(vcf_file, config)
    return out_file