code: def standard_cl_params(items):
      
      out = []
      def _skip_duplicates(data):
          return (dd.get_coverage_interval(data) == "amplicon" or
                  (dd.get_aligner(data) and not dd.get_mark_duplicates(data)))
      if any(_skip_duplicates(d) for d in items):
          broad_runner = broad.runner_from_config(items[0]["config"])
          gatk_type = broad_runner.gatk_type()
          if gatk_type == "gatk4":
              out += ["--disable-read-filter", "NotDuplicateReadFilter"]
          elif LooseVersion(broad_runner.gatk_major_version()) >= LooseVersion("3.5"):
              out += ["-drf", "DuplicateRead"]
      return out
docs: Shared command line parameters for GATK programs.
  
      Handles no removal of duplicate reads for amplicon or
      non mark duplicate experiments. If we have pre-aligned inputs we
      ignore the value or mark duplicates (since they may already be
      marked in the input BAM).