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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def _shared_gatk_call_prep(align_bams, items, ref_file, region, out_file, num_cores=1):
 """Shared preparation work for GATK variant calling. """

    data = items[0]
    config = data["config"]
    broad_runner = broad.runner_from_config(config)
    gatk_type = broad_runner.gatk_type()
    for x in align_bams:
        bam.index(x, config)
    picard_runner = broad.runner_from_path("picard", config)
    picard_runner.run_fn("picard_index_ref", ref_file)
    params = ["-R", ref_file]
    coverage_depth_min = tz.get_in(["algorithm", "coverage_depth_min"], config)
    if coverage_depth_min and coverage_depth_min < 4:
        confidence = "4.0"
        params += ["--standard_min_confidence_threshold_for_calling", confidence]
    for a in annotation.get_gatk_annotations(config):
        params += ["--annotation", a]
    for x in align_bams:
        params += ["-I", x]
    variant_regions = bedutils.population_variant_regions(items)
    region = subset_variant_regions(variant_regions, region, out_file, items)
    if region:
        if gatk_type == "gatk4":
            params += ["-L", bamprep.region_to_gatk(region), "--interval-set-rule", "INTERSECTION"]
        else:
            params += ["-L", bamprep.region_to_gatk(region), "--interval_set_rule", "INTERSECTION"]
    params += standard_cl_params(items)
    return broad_runner, params