First of all, the IRS Form 1040 NR you use is only for non-residents and the TurboTax program is only designed for US citizens and residents. These are two completely different tax forms with two distinct sets of tax laws. The rules for claiming certain tax credits and deductions, exemptions and tax rates are not the same.
If your spouse has had a J-1 visa for 2017 and 2018, she is considered as non-resident for those two years and required to file a Form 1040-NR. Starting from January, 1st 2019, if she has stayed physically for more than 183 days within the US regardless of her visa status, she is a US resident for tax purposes.
If you are a US citizen or resident, you both can file jointly on a normal US return Form 1040 just like other Americans by using one of the TurboTax programs. Please note that the TurboTax program only available for US citizens or residents to file, not non-residents.
To read more information between residents and nonresident, click here: Differences
I hope this helps.
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