Married filing separate is usually the highest tax rate, so you probably will pay more with this as your filing status. You both can't claim the same children on your tax return, so if you claim them on your W-4 but not on your return, you may wind up owing money next year. While we can't predict the outcome with certainty, it would probably make sense for you to use "Married, but withhold at the higher single rate."
You may have valid reasons for filing a separate return, but you can still file a joint return as long as you are married, and if you can both agree to it, it's usually the best choice.
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