def gatk_indel_realignment_cl(runner, align_bam, ref_file, intervals,
                              tmp_dir, region=None, deep_coverage=False,
                              known_vrns=None):
    """Prepare input arguments for GATK indel realignment.
    """
    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)
Prepare input arguments for GATK indel realignment.