code: def _add_tumor_params(paired, items, gatk_type):
      
      params = []
      if not paired:
          raise ValueError("Specified MuTect2 calling but 'tumor' phenotype not present in batch\n"
                           "https://bcbio-nextgen.readthedocs.org/en/latest/contents/"
                           "pipelines.html#cancer-variant-calling\n"
                           "for samples: %s" % ", " .join([dd.get_sample_name(x) for x in items]))
      if gatk_type == "gatk4":
          params += ["-I", paired.tumor_bam]
          params += ["--tumor-sample", paired.tumor_name]
      else:
          params += ["-I:tumor", paired.tumor_bam]
      if paired.normal_bam is not None:
          if gatk_type == "gatk4":
              params += ["-I", paired.normal_bam]
              params += ["--normal-sample", paired.normal_name]
          else:
              params += ["-I:normal", paired.normal_bam]
      if paired.normal_panel is not None:
          panel_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(items[0]), "mutect2", "panels"))
          normal_panel = vcfutils.bgzip_and_index(paired.normal_panel, items[0]["config"], out_dir=panel_dir)
          if gatk_type == "gatk4":
              params += ["--panel-of-normals", normal_panel]
          else:
              params += ["--normal_panel", normal_panel]
      return params
docs: Add tumor/normal BAM input parameters to command line.