Not necessarily. While generally speaking, filing jointly yields a better result than separate, this is one situation where you might get a better result filing separately, because only her income is considered for the penalty instead of both of yours. Double check the combined result (don't be fooled by just the apparent savings on one return, but rather add the two together). If you are getting greater savings filing separately, then use that method. (Comment if you are from a community property state, however, because that can complicate things if you file separately).
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