code: def pon_to_bed(pon_file, out_dir, data):
      
      out_file = os.path.join(out_dir, "%s-intervals.bed" % (utils.splitext_plus(os.path.basename(pon_file))[0]))
      if not utils.file_uptodate(out_file, pon_file):
          import h5py
          with file_transaction(data, out_file) as tx_out_file:
              with h5py.File(pon_file, "r") as f:
                  with open(tx_out_file, "w") as out_handle:
                      intervals = f["original_data"]["intervals"]
                      for i in range(len(intervals["transposed_index_start_end"][0])):
                          chrom = intervals["indexed_contig_names"][intervals["transposed_index_start_end"][0][i]]
                          start = int(intervals["transposed_index_start_end"][1][i]) - 1
                          end = int(intervals["transposed_index_start_end"][2][i])
                          out_handle.write("%s\t%s\t%s\n" % (chrom, start, end))
      return out_file
docs: Extract BED intervals from a GATK4 hdf5 panel of normal file.