def _varscan_work(align_bams, ref_file, items, target_regions, out_file):
    """Perform SNP and indel genotyping with VarScan.
    """
    config = items[0]["config"]

    orig_out_file = out_file
    out_file = orig_out_file.replace(".vcf.gz", ".vcf")

    max_read_depth = "1000"
    sample_list = _create_sample_list(align_bams, out_file)
    mpileup = samtools.prep_mpileup(align_bams, ref_file, config, max_read_depth,
                                    target_regions=target_regions, want_bcf=False)
    # VarScan fails to generate a header on files that start with
    # zerocoverage calls; strip these with grep, we're not going to
    # call on them
    remove_zerocoverage = r"{ ifne grep -v -P '\t0\t\t$' || true; }"
    # we use ifne from moreutils to ensure we process only on files with input, skipping otherwise
    # http://manpages.ubuntu.com/manpages/natty/man1/ifne.1.html
    with tx_tmpdir(items[0]) as tmp_dir:
        jvm_opts = _get_jvm_opts(config, tmp_dir)
        opts = " ".join(_varscan_options_from_config(config))
        min_af = float(utils.get_in(config, ("algorithm", "min_allele_fraction"), 10)) / 100.0
        fix_ambig_ref = vcfutils.fix_ambiguous_cl()
        fix_ambig_alt = vcfutils.fix_ambiguous_cl(5)
        py_cl = os.path.join(os.path.dirname(sys.executable), "py")
        export = utils.local_path_export()
        cmd = ("{export} {mpileup} | {remove_zerocoverage} | "
               "ifne varscan {jvm_opts} mpileup2cns {opts} "
               "--vcf-sample-list {sample_list} --min-var-freq {min_af} --output-vcf --variants | "
               """{py_cl} -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "{ref_file}")' | """
               "{py_cl} -x 'bcbio.variation.varscan.fix_varscan_output(x)' | "
               "{fix_ambig_ref} | {fix_ambig_alt} | ifne vcfuniqalleles > {out_file}")
        do.run(cmd.format(**locals()), "Varscan", None,
                [do.file_exists(out_file)])
    os.remove(sample_list)
    # VarScan can create completely empty files in regions without
    # variants, so we create a correctly formatted empty file
    if os.path.getsize(out_file) == 0:
        write_empty_vcf(out_file)

    if orig_out_file.endswith(".gz"):
        vcfutils.bgzip_and_index(out_file, config)
Perform SNP and indel genotyping with VarScan.