code: def run(align_bams, items, ref_file, assoc_files, region, out_file):
      
      if not utils.file_exists(out_file):
          paired = vcfutils.get_paired_bams(align_bams, items)
          vrs = bedutils.population_variant_regions(items)
          target = shared.subset_variant_regions(vrs, region,
                                                 out_file, items=items, do_merge=True)
          if paired:
              return _run_somatic(paired, ref_file, target, out_file)
          else:
              return _run_germline(align_bams, items, ref_file, target, out_file)
      return out_file
docs: Run octopus variant calling, handling both somatic and germline calling.