code: def _do_merge(orig_files, out_file, config, region):
      
      if not utils.file_exists(out_file):
          with file_transaction(config, out_file) as tx_out_file:
              _check_samples_nodups(orig_files)
              prep_files = run_multicore(p_bgzip_and_index, [[x, config] for x in orig_files], config)
              input_vcf_file = "%s-files.txt" % utils.splitext_plus(out_file)[0]
              with open(input_vcf_file, "w") as out_handle:
                  for fname in prep_files:
                      out_handle.write(fname + "\n")
              bcftools = config_utils.get_program("bcftools", config)
              output_type = "z" if out_file.endswith(".gz") else "v"
              region_str = "-r {}".format(region) if region else ""
              cmd = "{bcftools} merge -O {output_type} {region_str} `cat {input_vcf_file}` > {tx_out_file}"
              do.run(cmd.format(**locals()), "Merge variants")
      if out_file.endswith(".gz"):
          bgzip_and_index(out_file, config)
      return out_file
docs: Do the actual work of merging with bcftools merge.