The standard deduction of $12,550 is automatically applied when you choose Married Filing a separate return and indicate that your spouse is NOT itemizing their return. If they are itemizing their return, you cannot get the standard deduction, you would need to take the itemized deduction as well.
Filing a joint return saves some people money, but not everyone. Many people, especially those without kids and that have income above a level where they do not qualify for the Earned Income Tax Credit, make out better filing separate returns.
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