def fix_ambiguous_cl(column=4):
    """awk command to replace non-N ambiguous REF bases with N.

    Some callers include these if present in the reference genome but GATK does
    not like them.
    """
    return r"""awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $%s) } {print}'""" % column