You start by entering your 1099-INT into the system just as it was issued to you. Then, after you have entered the 1099-INT, there is a screen that says "Do any of these uncommon situations apply?" and you will check the box that says "I need to adjust the interest reported on my form". That will give you a box to enter the amount and a drop down menu to select 'Accrued Market Discount'. That should take care of it for you.
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