Generally, you cannot file as married filing jointly if either spouse was a nonresident alien at any time during the tax year.

Yes, a nonresident alien students who, at the time of their arrival in the United States, intend to reside in the United States for longer than 1 year are subject to the 30 percent taxation on their U.S. source capital gains during any tax year in which they are present in the United States for 183 days or more, unless a tax treaty provides for a lesser rate of taxation. Please see IRS he Taxation of Capital Gains of Nonresident Alien Students for more details.

TurboTax does not support Form 1040NR for a non-resident.  You can prepare your return through a company we partner with called Sprintax. 

This is what I got from your expert.

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Dear TurboTax Customer,

Thank you for contacting TurboTax Support.

Here is the information we discussed during our call:

If there is no ITIN or SSN, then in any place where the nonresident spouse's taxpayer ID number is required on a tax form, you would take a black or blue pen and manually write "nonresident alien" or abbreviate as "NRA."  In the TurboTax software, you can input any "made up" SSN or ITIN you want to, in order get through the program (we suggest [social security number removed], [social security number removed] or [social security number removed], as those numbers won’t produce any TurboTax program errors in a review check) as a temporary "placeholder.”  You can then later "white out" that number when the paper pages are printed.

https://turbotax.intuit.com/tax-tips/family/claiming-a-non-citizen-spouse-and-children-on-your-taxes...

https://ttlc.intuit.com/community/taxes/discussion/non-resi[product key removed]e-how-to-file/00/156...
 

I would like to make sure this has been completely resolved for you. Should you need to contact us again about this situation, you may use case number [social security number removed] as the Support ID.  

Thank you,

Nicole S.

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And actually, it's not working as well. I'm very disappointed and confused you have different workflow and didn't even to make any investigation. 

I got answer from other tax agent.

Here is the IRS link: 

Basically, my spouse just needs to file w7 to apply ITIN together with the tax return filing. 

In your original post you had stated that you are in the 5 year of your F1 visa. F-1 visa holders are not considered residents until their 6th calendar year in the United States.  At that point, the Substantial Presence Test would need to be met to be considered a resident. Please see IRS Alien Residency Examples for additional information.  Therefore, you need to file Form 1040NR which doesn't allow you file jointly. You will have to use Sprintax. 

If you are already in your 6th year and met the Substantial Presence Test then you can file Form 1040 and choose to treat your spouse as a resident for tax purposes (if she hasn't met the Substantial Presence Test herself since she is also exempt for 5 years on the F2 visa).

Please be aware, that each spouse must report his or her entire worldwide income for the year you make the choice and for all later years, unless the choice is ended or suspended.

To make the choice attach a statement to your paper return (you can't e-file), signed by both spouses, to your joint return for the first tax year for which the choice applies. It should contain the following information:

1. A declaration that one spouse was a nonresident alien and the other spouse a U.S. citizen or resident alien on the last day of the tax year, and that you choose to be treated as U.S. residents for the entire tax year
2. The name, address, and identification number of each spouse. (If one spouse died, include the name and address of the person making the choice for the deceased spouse.)

Please see IRS Nonresident Alien Spouse for more details.

You will need to apply for an Individual Taxpayer Identification Number (ITIN) for your spouse. Please see How do I apply for an ITIN?

If you both are in your 6th year or later and have met the Substantial Presence Test then all you have to do is apply for the ITIN for your spouse.