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On J1 as a research scholar you are non-resident aliens for 2 calendar years, so 2015 and 2016. As a nonresident alien you would need to file form 1040NR plus form 8843 as married filing separately, nonresident aliens cannot file joint returns (with very few exceptions). Turbotax does not provide these forms.
Since you filed the wrong return, you will also need to amend your return for 2015. You will need to fill out the correct return and add form 1040X to it. Also add an explanation of your error to it (as it is usually not possible to amend from filing jointly to separately).
First do the amendment and then file a correct return for 2016. Also, the institutions are wrong in their advice to file single, that is not an option when you are married. May I ask which institution that is? (I was a postdoc at Harvard and they did a lot of mistakes with aliens).
There might also be a tax treaty with your country of origin that you might be able to claim. Where are you both from?
Have a look at publication 519 and feel free to ask follow up questions.
On J1 as a research scholar you are non-resident aliens for 2 calendar years, so 2015 and 2016. As a nonresident alien you would need to file form 1040NR plus form 8843 as married filing separately, nonresident aliens cannot file joint returns (with very few exceptions). Turbotax does not provide these forms.
Since you filed the wrong return, you will also need to amend your return for 2015. You will need to fill out the correct return and add form 1040X to it. Also add an explanation of your error to it (as it is usually not possible to amend from filing jointly to separately).
First do the amendment and then file a correct return for 2016. Also, the institutions are wrong in their advice to file single, that is not an option when you are married. May I ask which institution that is? (I was a postdoc at Harvard and they did a lot of mistakes with aliens).
There might also be a tax treaty with your country of origin that you might be able to claim. Where are you both from?
Have a look at publication 519 and feel free to ask follow up questions.
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