code: def concat_variant_files(orig_files, out_file, regions, ref_file, config):
      
      if not utils.file_exists(out_file):
          input_file_list = _get_file_list(orig_files, out_file, regions, ref_file, config)
          try:
              out_file = _run_concat_variant_files_gatk4(input_file_list, out_file, config)
          except subprocess.CalledProcessError as msg:
              if ("We require all VCFs to have complete VCF headers" in str(msg) or
                    "Features added out of order" in str(msg) or
                    "The reference allele cannot be missing" in str(msg)):
                  out_file = _run_concat_variant_files_bcftools(input_file_list, out_file, config, naive=True)
              else:
                  raise
      if out_file.endswith(".gz"):
          bgzip_and_index(out_file, config)
      return out_file
docs: Concatenate multiple variant files from regions into a single output file.
  
      Uses GATK4's GatherVcfs, falling back to bcftools concat --naive if it fails.
      These both only combine samples and avoid parsing, allowing scaling to large
      file sizes.