Get your taxes done using TurboTax

Yes, it will raise a red flag if your wife takes the standard deduction and you itemize. In your wife's return, go back to the beginning of the Personal Info or Your Info section, where you enter her name and other details. Make sure that you selected Married for her marital status, and that you said No where it asks if she wants to file together with her spouse. Then go to where you entered your name and Social Security number in your wife's return, as the spouse. You will come to the screen shown below. Check the box that says "Either my spouse or I claim itemized deductions." That will force the return to use itemized deductions. You should check that box for both returns.