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You could file joint for federal and then still file your state returns with just your own resident income listed on your own state returns.
For instance in Colorado, a resident taxpayer and nonresident or part-year resident spouse must file a joint Colorado income tax return if they file a joint federal income tax return. Use the nonresident or part-year resident tax computation rules found on Form 104PN. This form can also be found in the Individual Income Tax Booklet (104). Both the 104 and the 104PN schedule must be completed and filed with the Colorado Department of Revenue.
Neither of you can file as a single filer. You can file joint or married filing separate.
If you choose joint then you each only report in your state the correct income for that specific state but not all your income as you show on federal combined.
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