Get your taxes done using TurboTax

I was talking about my 2021 tax year. I filed as HoH and spouse file as separate because she lived in another state.  Though it was easier because TurboTax was unable to handle my investment  Now I found out we should have considered the joint filing (less tax and probably less penalty because I missed the deadline. Can I call the IRS and ask to amend ? or just pay what IRS is asking and then file a new amended return ?