I was audited, they changed my filing status to married filing separate, they disallowed some of my income. I have not signed the 4549 because I now have proof of income that I did not have before, and I want to change filing status to married filing joint, because I was told if I was married for 6 months that I can file married filing joint.

I am thinking that it might solve the whole thing to ammend and change my filing status, as well as include the unincluded income and send it back with the unsigned 4549.

Is that the way to handle it or is there a better way.

To file MFJ your spouse must be willing to sign a joint return. Is your spouse willing to do this? Also where you married on the last day of the tax year? What reason did the IRS give you for wanting to change your filing status from you original choice to MFS? Yes you can dispute the IRS findings with your new proof of income.

yes we were married at the end of the year and still are. Just did not think we could claim moj if we were not married for 6 months, were got married on june 3 2016 and had a wedding seremony on july 14 2016, there were reasons for this that I will not go into. She is willing to sign the return. Glad I can add the new income. So do I do an amended and send it with the documentation for the income and the unsigned disputed 4549? Is that how I should handle it or is there a different route to handle it.

You asked why did they change it to filing separate, because I did not claim her as a dependent and sent them copies of the marriage license and marriage certificate.

As you are already under audit I think I would make a whole new tax return (rather than an amended 1040X) and attach to the 4549 all the pages that changed from the original (which is all of them as your filing status is changing). State these are the changes you propose. Explane the reason for the changes (the original return had the wrong filing status and did not include the following income items). I would include a cover letter expaning everything. P.S. a husband and wife (or any spouses) do not "normally" claim a dependency exemption for each other. They each get a personal exemtion.

Thanks so much for all of the info, I really do appreciate it as I was unsure how to handle it.