My home of record is in the state of West Virginia. But I'm a military member who lives in japan

If you spent less than 30 days in WV in 2016, your military pay is exempt from WV tax; if you were in WV for more than 30 days, it is taxable. You remain a resident of WV and have to file a WV tax return.

The WV state interview in TurboTax will ask the appropriate questions to determine what category you are in.

From the WV 2016 Tax Booklet, page 17:

 If your legal residence was West Virginia at the time you entered military service, assignment to duty outside the state does not change your West Virginia residency status. You must file your return and pay the tax due in the same manner as any other resident individual unless you did not maintain a physical presence in West Virginia for more than 30 days during the taxable year.

If, during 2016, you spent more than 30 days in West Virginia,you are considered to be a West Virginia resident for income tax purposes and must file a resident return and report all of your income to West Virginia.