You will have to file as Married- either jointly or separate.
Generally, a married couple can't file a joint return if either one is a nonresident alien at any time during the tax year. However, if one spouse was a nonresident alien who was married to a U.S. citizen or resident alien at the end of the year, the spouses can choose to file a joint return. If you do file a joint return, you and your spouse are both treated as U.S. residents for the entire tax year. If you choose to file joint, she will have to get an Individual Taxpayer Identification Number if she cannot get a social security number. See Who Needs an ITIN?
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