code: def _run_delly(bam_files, chrom, ref_file, work_dir, items):
      
      batch = sshared.get_cur_batch(items)
      ext = "-%s-svs" % batch if batch else "-svs"
      out_file = os.path.join(work_dir, "%s%s-%s.bcf"
                              % (os.path.splitext(os.path.basename(bam_files[0]))[0], ext, chrom))
      final_file = "%s.vcf.gz" % (utils.splitext_plus(out_file)[0])
      cores = min(utils.get_in(items[0], ("config", "algorithm", "num_cores"), 1),
                  len(bam_files))
      if not utils.file_exists(out_file) and not utils.file_exists(final_file):
          with file_transaction(items[0], out_file) as tx_out_file:
              if sshared.has_variant_regions(items, out_file, chrom):
                  exclude = ["-x", _delly_exclude_file(items, out_file, chrom)]
                  cmd = ["delly", "call", "-g", ref_file, "-o", tx_out_file] + exclude + bam_files
                  multi_cmd = "export OMP_NUM_THREADS=%s && export LC_ALL=C && " % cores
                  try:
                      do.run(multi_cmd + " ".join(cmd), "delly structural variant")
                  except subprocess.CalledProcessError as msg:
                      # Small input samples, write an empty vcf
                      if "Sample has not enough data to estimate library parameters" in str(msg):
                          pass
                      # delly returns an error exit code if there are no variants
                      elif "No structural variants found" not in str(msg):
                          raise
      return [_bgzip_and_clean(out_file, items)]
docs: Run delly, calling structural variations for the specified type.