Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.

def _piped_realign_gatk(data, region, cl, out_base_file, tmp_dir, prep_params):
    """Perform realignment with GATK, using input commandline.
    GATK requires writing to disk and indexing before realignment.
    """
    broad_runner = broad.runner_from_config(data["config"])
    pa_bam = "%s-prealign%s" % os.path.splitext(out_base_file)
    if not utils.file_exists(pa_bam):
        with file_transaction(data, pa_bam) as tx_out_file:
            cmd = "{cl} -o {tx_out_file}".format(**locals())
            do.run(cmd, "GATK re-alignment {0}".format(region), data)
    bam.index(pa_bam, data["config"])
    realn_file = realign.gatk_realigner_targets(broad_runner, pa_bam, dd.get_ref_file(data), data["config"],
                                                region=region_to_gatk(region),
                                                known_vrns=dd.get_variation_resources(data))
    realn_cl = realign.gatk_indel_realignment_cl(broad_runner, pa_bam, dd.get_ref_file(data),
                                                 realn_file, tmp_dir, region=region_to_gatk(region),
                                                 known_vrns=dd.get_variation_resources(data))
    return pa_bam, realn_cl