code: def _gatk_extract_reads_cl(data, region, prep_params, tmp_dir):
      
      args = ["PrintReads",
              "-L", region_to_gatk(region),
              "-R", dd.get_ref_file(data),
              "-I", data["work_bam"]]
      # GATK3 back compatibility, need to specify analysis type
      if "gatk4" in dd.get_tools_off(data):
          args = ["--analysis_type"] + args
      runner = broad.runner_from_config(data["config"])
      return runner.cl_gatk(args, tmp_dir)
docs: Use GATK to extract reads from full BAM file.