code: def _create_vcf(root_file, out_file, reference, items, paired=None):
      
      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
docs: 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