Perform SNP genotyping on the given alignment file.

def unified_genotyper(align_bams, items, ref_file, assoc_files,
                       region=None, out_file=None):
    """Perform SNP genotyping on the given alignment file.
    """
    if out_file is None:
        out_file = "%s-variants.vcf.gz" % utils.splitext_plus(align_bams[0])[0]
    if not utils.file_exists(out_file):
        broad_runner, params = \
            _shared_gatk_call_prep(align_bams, items, ref_file, region, out_file)
        with file_transaction(items[0], out_file) as tx_out_file:
            params += ["-T", "UnifiedGenotyper",
                       "-o", tx_out_file,
                       "-ploidy", (str(ploidy.get_ploidy(items, region))
                                   if broad_runner.gatk_type() == "restricted" else "2"),
                       "--genotype_likelihoods_model", "BOTH"]
            resources = config_utils.get_resources("gatk", items[0]["config"])
            if "options" in resources:
                params += [str(x) for x in resources.get("options", [])]
            broad_runner.run_gatk(params)
    return vcfutils.bgzip_and_index(out_file, items[0]["config"])