code: def _add_somatic_opts(opts, paired):
      
      if "--min-alternate-fraction" not in opts and "-F" not in opts:
          # add minimum reportable allele frequency
          # FreeBayes defaults to 20%, but use 10% by default for the
          # tumor case
          min_af = float(utils.get_in(paired.tumor_config, ("algorithm",
                                                            "min_allele_fraction"), 10)) / 100.0
          opts += " --min-alternate-fraction %s" % min_af
      # Recommended settings for cancer calling
      opts += (" --pooled-discrete --pooled-continuous "
               "--report-genotype-likelihood-max --allele-balance-priors-off")
      return opts
docs: Add somatic options to current set. See _run_freebayes_paired for references.