code: def parallel_combine_variants(orig_files, out_file, ref_file, config, run_parallel):
      
      file_key = "vcf_files"
      def split_by_region(data):
          base, ext = utils.splitext_plus(os.path.basename(out_file))
          args = []
          for region in [x.name for x in ref.file_contigs(ref_file, config)]:
              region_out = os.path.join(os.path.dirname(out_file), "%s-regions" % base,
                                        "%s-%s%s" % (base, region, ext))
              utils.safe_makedir(os.path.dirname(region_out))
              args.append((region_out, ref_file, config, region))
          return out_file, args
      config = copy.deepcopy(config)
      config["file_key"] = file_key
      prep_files = run_multicore(p_bgzip_and_index, [[x, config] for x in orig_files], config)
      items = [[{file_key: prep_files}]]
      parallel_split_combine(items, split_by_region, run_parallel,
                             "merge_variant_files", "concat_variant_files",
                             file_key, ["region", "sam_ref", "config"], split_outfile_i=0)
      return out_file
docs: Combine variants in parallel by chromosome, concatenating final outputs.