code: def _bcftools_stats(data, out_dir, vcf_file_key=None, germline=False):
      
      vcinfo = get_active_vcinfo(data)
      if vcinfo:
          out_dir = utils.safe_makedir(out_dir)
          vcf_file = vcinfo[vcf_file_key or "vrn_file"]
          if dd.get_jointcaller(data) or "gvcf" in dd.get_tools_on(data):
              opts = ""
          else:
              opts = "-f PASS,."
          name = dd.get_sample_name(data)
          out_file = os.path.join(out_dir, "%s_bcftools_stats%s.txt" % (name, ("_germline" if germline else "")))
          bcftools = config_utils.get_program("bcftools", data["config"])
          if not utils.file_exists(out_file):
              with file_transaction(data, out_file) as tx_out_file:
                  orig_out_file = os.path.join(os.path.dirname(tx_out_file), "orig_%s" % os.path.basename(tx_out_file))
                  cmd = ("{bcftools} stats -s {name} {opts} {vcf_file} > {orig_out_file}")
                  do.run(cmd.format(**locals()), "bcftools stats %s" % name)
                  with open(orig_out_file) as in_handle:
                      with open(tx_out_file, "w") as out_handle:
                          for line in in_handle:
                              if line.startswith("ID\t"):
                                  parts = line.split("\t")
                                  parts[-1] = "%s\n" % name
                                  line = "\t".join(parts)
                              out_handle.write(line)
          return out_file
docs: Run bcftools stats.