As mentioned by @BrigiMario, if you choose to file a joint return you cannot pick and choose which income to include. All income must be included.
If she files a separate return and has taxes withheld, as long as you are not taking an itemized deduction, she would get a full refund of everything she had withheld for federal (state laws vary)
When you file separate you make be disqualified for certain tax credits, but running it both ways first is the best way to figure out which way you should file.
You can switch back and forth each year.
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