Add parameters based on configuration variables, associated files and genomic regions.

def _config_params(base_config, assoc_files, region, out_file, items):
    """Add parameters based on configuration variables, associated files and genomic regions.
    """
    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