You have to prepare a seperate federal tax return to do the state filing as married-separate. If you are working online with TurboTax, you will have to set up a new account and enter just one spouse's information in the federal section and then do the state return filing as married-separate. You can e-file the state return but don't file the federal return as you have already done that in the other program where you filed married-joint.
If you use the desktop version of TurboTax, you can prepare and file multiple returns using the same program.
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