Thanks for asking your question! I'm sorry to hear about your tax issue and I'm going to try my best to help you understand or resolve it.
Thanks for your question. Your wife will need to file an amended tax return, as she can only file married filing joint or married filing separately. She cannot file a single return as she was married as of the last day of the tax year.
If you wanted to file a joint return together, your information will need to be on the amended tax return.
Here is an extract from Form 1040X instructions for your reference-Changing from separate to a joint return.
If you and your spouse are changing from separate returns to a joint return, follow these steps.
Enter in column A the amounts from your return as originally filed or as previously adjusted (either by you or the IRS).
Combine the amounts from your spouse's return as originally filed or as previously adjusted with any other changes you or your spouse are making to determine the amounts to enter in column B. If your spouse did not file an original return, include your spouse's income, deductions, credits, other taxes, etc., to determine the amounts to enter in column B.
Read the instructions for column C on this page to figure the amounts to enter in that column.
Both of you must sign Form 1040X.
Please let me know if you need anything additional. Thanks again for using JustAnswer.com and have a great day.
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You should be aware that your question, as with most tax questions, can never really be answered completely...addressing all the permutations; that is because of the many assumptions that have to be made I have done my best to determine what I think you are asking and answering it in the most direct and understandable manner possible. If, however, after reviewing the questions, you have any uncertainties or further questions, please do not hesitate to ask.