If you are married and file separately, enter on each return the share of mortgage interest for each spouse. The sum of the two must equal to the amount on form 1098. The split does not need to be 50/50.
But remember that both spouses must have the same deduction option. If one spouse uses itemized deductions, the other spouse must also use itemized deductions, even if they total less than the standard deduction. Or both spouses can use the standard deduction.
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