West Virginia requires you to file a nonresident return and pay state income tax on your wages for your job in West Virginia (WV). You should prepare this WV nonresident tax return first, if possible.
The West Virginia nonresident return calculates taxes as if all your income was taxed in West Virginia, and then applies the percentage of your West Virginia income to your total income, to prorate to you only the tax related to your WV income. As long as your West Virginia income is properly identified when you work through your WV nonresident return, TurboTax will calculate the tax correctly.
Virginia (VA) also requires you to report as income the wages earned in West Virginia but will give you a credit for WV tax you paid on that same income. Be sure to look for that credit when you prepare the VA return.
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