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If you file married filing separate then all your SS base for determining taxable portion is $0. That may make you pay tax on your SS benefits if you have other income yourself.
The best way to tell if a couple should file joint or separate is to prepare the returns both ways. That is the only way to know for certain. So first do your returns joint then do your return separate and see if you owe more one way or the other before you both decide how you wish to file.