Yes. TurboTax can handle your situation. Since you mentioned you had stocks, you might want to use the Premier version.
1. If you had been present within the US on an F-visa for five years by the end of 2018, and because you have been in the US for more than 183 days in 2019, you are considered as a US resident for tax purposes starting from the year 2019. You start counting days from January 1st, 2019.
2. You are only exempt from FICA taxes for five years while you were on F-visa. You are subject to pay FICA starting from January 1st, 2019. See information from the IRS: FICA for F-1 visa holders under " The Social Security/Medicare and Self-Employment Tax Liability of Foreign Students, Scholars Teachers, Researchers, and Trainees" TurboTax does not handle the complexity of the FICA taxes for nonresidents, unfortunately.
I would suggest you communicate with your employer to resolve the issues. They might need to issue you a corrected 2019 W-2 thus you may need to amend your tax return later. I am including a post from user Lisa Br who provided a very helpful answer to the same question. Click here FICA withholding
3. Since you are a US resident for tax purposes, you can make an election to claim your nonresident spouse as a resident and file jointly. For more information, click here: Nonresident to resident You won't be able to e-file your return. Instead, you would need to print out required tax forms and submit them along with the election ( a statement) to the IRS.
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