code: def _prep_callable_bed(in_file, work_dir, stats, data):
      
      out_file = os.path.join(work_dir, "%s-merge.bed.gz" % utils.splitext_plus(os.path.basename(in_file))[0])
      gsort = config_utils.get_program("gsort", data)
      if not utils.file_uptodate(out_file, in_file):
          with file_transaction(data, out_file) as tx_out_file:
              fai_file = ref.fasta_idx(dd.get_ref_file(data))
              cmd = ("{gsort} {in_file} {fai_file} | bedtools merge -i - -d {stats[merge_size]} | "
                     "bgzip -c > {tx_out_file}")
              do.run(cmd.format(**locals()), "Prepare SV callable BED regions")
      return vcfutils.bgzip_and_index(out_file, data["config"])
docs: Sort and merge callable BED regions to prevent SV double counting