code: def _run_concat_variant_files_bcftools(in_list, out_file, config, naive=False):
      
      if not utils.file_exists(out_file):
          with file_transaction(config, out_file) as tx_out_file:
              bcftools = config_utils.get_program("bcftools", config)
              output_type = "z" if out_file.endswith(".gz") else "v"
              if naive:
                  args = "--naive"
              else:
                  args = "--allow-overlaps"
              cmd = "{bcftools} concat {args} -O {output_type} --file-list {in_list} -o {tx_out_file}"
              do.run(cmd.format(**locals()), "bcftools concat variants")
      if out_file.endswith(".gz"):
          bgzip_and_index(out_file, config)
      return out_file
docs: Concatenate variant files using bcftools concat, potentially using the fast naive option.