One thing I want to correct after re-reading my previous reply---no matter whether you lived apart or lived together during the tax year, if you were legally married at the end of the tax year, your filing choices are married filing jointly or married filing separately. If you lived apart for at least the last six months of the tax year and do not want to file a joint return, you may file as head of household if you are the custodial parent of the children.
Still not sure what you are trying to do in regard to the fact that your spouse was in a different state.
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