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Get your taxes done using TurboTax
If the kids belong to both of you and lived at least half the year with both of you, then you are both custodial parents. If that's the case, then technically your wife has the right to file MFS and to claim the children. What she can't do is file HOH, as others have explained. A married taxpayer living with their spouse cannot file HOH.
Form 3949 is not appropriate for this situation.
If you're the father, you also have the right to claim the children since you too are a custodial parent.
So - as others have said - your only recourse is to paper-file your return as MFS and claim the kids.
When the IRS receives two returns, each claiming the same dependents, it will apply its own tie-breaker rules. Winner gets the tax benefits; loser's return and tax bill get adjusted accordingly, including possible interest and penalties.
Filing MFS is costing you both considerable money, so the ideal outcome would be for you to convince her to file an amended return and to file MFJ.