Yes, if you're in a Community Property state and filing as MFS, TurboTax will automatically split the deduction.
However, you can change the amounts. If only one person was responsible for the mortgage payment then that person would claim the mortgage interest. If it was paid out of a joint account, then you would split the amount between the two of you, entering half on each of your returns.
The person who is listed second will select "My name is not on the 1098, or my name isn't the first one listed". Remember, if one person itemizes you both must itemize as the other person cannot take the standard deduction.
Here's more info on Married Filing Separately and How to Compare MFS/MFJ if you're using TurboTax Desktop.
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