You will want to file using the method that gives you the lowest tax liability as a family unit. The only way to know for sure is to create test returns, one for each spouse, and compare the bottom lines. Be sure to also prepare the state return so you can get a complete tax picture.
If you use TurboTax CD/Download there's is a quick way to get a comparison. This link https://How can we compare married filing jointly with married filing separately? has information you may find useful if you use the CD/Download version.
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