You can file jointly at the federal level but married filing separately at the state level. But which states?
Rules that govern home state are complicated. Check this information about state of residence from military.com.
If you got a driver's license in SC, registered to vote in SC, and/or actually voted in SC, then you are a resident of SC and must pay income tax to that state.
If you qualify as the resident of another state, then you can file an amended 2015 SC return to get a refund.
State rules that apply to paying taxes in the home state versus the state where you have PCS orders can be found below.
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