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After you file
xmasbaby0 is correct - if you believe that the IRS's position is incorrect, you should challenge it or at the very least, discuss it with a tax professional.
Sometimes the IRS makes a mistake because through no fault of theirs, they don't have all the information needed.
Whatever you do, please respond to the IRS in a timely fashion (generally in about three weeks), even if you haven't finished collecting the facts yet. Note that an Enrolled Agent or a CPA can represent you in the discussion with the IRS and, depending on the facts of the case, may even negotiate for an abatement (waiver) of penalties and/or interest even if you end up owning the tax.
Enrolled Agents are regulated directly by the IRS; you can find one near you at https://taxexperts.naea.org/ . CPAs are regulated by each state; you can do an Internet Search on "CPA State Board" and your state's name - every state surely has a way to look up local CPAs.