code: def _mutect_call_prep(align_bams, items, ref_file, assoc_files,
                         region=None, out_file=None):
      
      base_config = items[0]["config"]
      broad_runner = broad.runner_from_path("picard", base_config)
      broad_runner.run_fn("picard_index_ref", ref_file)
  
      broad_runner = broad.runner_from_config(base_config, "mutect")
      _check_mutect_version(broad_runner)
      for x in align_bams:
          bam.index(x, base_config)
  
      paired = vcfutils.get_paired_bams(align_bams, items)
      if not paired:
          raise ValueError("Specified MuTect 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]))
      params = ["-R", ref_file, "-T", "MuTect", "-U", "ALLOW_N_CIGAR_READS"]
      params += ["--read_filter", "NotPrimaryAlignment"]
      params += ["-I:tumor", paired.tumor_bam]
      params += ["--tumor_sample_name", paired.tumor_name]
      if paired.normal_bam is not None:
          params += ["-I:normal", paired.normal_bam]
          params += ["--normal_sample_name", paired.normal_name]
      if paired.normal_panel is not None:
          params += ["--normal_panel", paired.normal_panel]
      params += _config_params(base_config, assoc_files, region, out_file, items)
      return broad_runner, params
docs: Preparation work for MuTect.