code: def _config_params(base_config, assoc_files, region, out_file, items):
      
      params = []
      dbsnp = assoc_files.get("dbsnp")
      if dbsnp:
          params += ["--dbsnp", dbsnp]
      cosmic = assoc_files.get("cosmic")
      if cosmic:
          params += ["--cosmic", cosmic]
      variant_regions = bedutils.population_variant_regions(items)
      region = subset_variant_regions(variant_regions, region, out_file, items)
      if region:
          params += ["-L", bamprep.region_to_gatk(region), "--interval_set_rule",
                     "INTERSECTION"]
      # set low frequency calling parameter if adjusted
      # to set other MuTect parameters on contamination, pass options to resources for mutect
      # --fraction_contamination --minimum_normal_allele_fraction
      min_af = tz.get_in(["algorithm", "min_allele_fraction"], base_config)
      if min_af:
          params += ["--minimum_mutation_cell_fraction", "%.2f" % (min_af / 100.0)]
      resources = config_utils.get_resources("mutect", base_config)
      if resources.get("options") is not None:
          params += [str(x) for x in resources.get("options", [])]
      # Output quality scores
      if "--enable_qscore_output" not in params:
          params.append("--enable_qscore_output")
      # drf not currently supported in MuTect to turn off duplicateread filter
      # params += gatk.standard_cl_params(items)
      return params
docs: Add parameters based on configuration variables, associated files and genomic regions.