The TurboTax program will recommend the standard deduction or the itemized deduction. It may not be a good for you to itemize deductions since you are filing as married filing separately as your wife will be required to itemize her deductions (even if she has no deductions).
In most cases it is better to file using the married filing joint filing status. Please view the TurboTax FAQ below for more information about choosing a filing status. It includes a link for you to compare which filing status would benefit you more.
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