code: def gatk_indel_realignment_cl(runner, align_bam, ref_file, intervals,
                                tmp_dir, region=None, deep_coverage=False,
                                known_vrns=None):
      
      if not known_vrns:
          known_vrns = {}
      params = ["-T", "IndelRealigner",
                "-I", align_bam,
                "-R", ref_file,
                "-targetIntervals", intervals,
                ]
      if region:
          params += ["-L", region]
      if known_vrns.get("train_indels"):
          params += ["--knownAlleles", known_vrns["train_indels"]]
      if deep_coverage:
          params += ["--maxReadsInMemory", "300000",
                     "--maxReadsForRealignment", str(int(5e5)),
                     "--maxReadsForConsensuses", "500",
                     "--maxConsensuses", "100"]
      return runner.cl_gatk(params, tmp_dir)
docs: Prepare input arguments for GATK indel realignment.