code: def _run_bcbio_variation(vrn_file, rm_file, rm_interval_file, base_dir, sample, caller, data):
      
      val_config_file = _create_validate_config_file(vrn_file, rm_file, rm_interval_file,
                                                     base_dir, data)
      work_dir = os.path.join(base_dir, "work")
      out = {"summary": os.path.join(work_dir, "validate-summary.csv"),
             "grading": os.path.join(work_dir, "validate-grading.yaml"),
             "discordant": os.path.join(work_dir, "%s-eval-ref-discordance-annotate.vcf" % sample)}
      if not utils.file_exists(out["discordant"]) or not utils.file_exists(out["grading"]):
          bcbio_variation_comparison(val_config_file, base_dir, data)
      out["concordant"] = filter(os.path.exists,
                                  [os.path.join(work_dir, "%s-%s-concordance.vcf" % (sample, x))
                                   for x in ["eval-ref", "ref-eval"]])[0]
      return out
docs: Run validation of a caller against the truth set using bcbio.variation.