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If the taxpayers were non-filers and now suddenly file their tax returns as married filing separately, does that raise a red flag with the IRS?

No, it does not. Remember, the default is married filing separately. Spouses are allowed to elect to file joint, but do not have to do so. Also remember that taxpayers can file separately and then amend to file joint. Once they file joint they CANNOT amend to file separately. So joint filing should only be done when it is to the couple\’s advantage to do so.

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