def _clean_varscan_line(line):
    """Avoid lines with non-GATC bases, ambiguous output bases make GATK unhappy.
    """
    if not line.startswith("#"):
        parts = line.split("\t")
        alleles = [x.strip() for x in parts[4].split(",")] + [parts[3].strip()]
        for a in alleles:
            if len(set(a) - set("GATCgatc")) > 0:
                return None
    return line