code: def normalize(in_file, data, passonly=False, normalize_indels=True, split_biallelic=True,
                rerun_effects=True, remove_oldeffects=False, nonrefonly=False, work_dir=None):
      
      if remove_oldeffects:
          out_file = "%s-noeff-nomultiallelic%s" % utils.splitext_plus(in_file)
      else:
          out_file = "%s-nomultiallelic%s" % utils.splitext_plus(in_file)
      if work_dir:
          out_file = os.path.join(work_dir, os.path.basename(out_file))
      if not utils.file_exists(out_file):
          if vcfutils.vcf_has_variants(in_file):
              ready_ma_file = _normalize(in_file, data, passonly=passonly,
                                         normalize_indels=normalize_indels,
                                         split_biallelic=split_biallelic,
                                         remove_oldeffects=remove_oldeffects,
                                         nonrefonly=nonrefonly,
                                         work_dir=work_dir)
              if rerun_effects:
                  ann_ma_file, _ = effects.add_to_vcf(ready_ma_file, data)
                  if ann_ma_file:
                      ready_ma_file = ann_ma_file
              utils.symlink_plus(ready_ma_file, out_file)
          else:
              utils.symlink_plus(in_file, out_file)
      return vcfutils.bgzip_and_index(out_file, data["config"])
docs: Normalizes variants and reruns SnpEFF for resulting VCF