USA 2012 tax return Issue

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Hello All -

I am an Indian Citizen on H1 B visa working in USA.

I had come to US on July 18, 2012 and was here until December 7, 2012 (141 days exluding first and last day). During this time I was single. I got married on Dec 15, 2012. Then I returned to US on Jan 09, 2013.

Initially, my tax preparer filed my tax returns in March 2013. At that time he had filed form 1040 with Single status for me.
And once my wife came to US, they filed Amendment 1040X with married filing jointly status.

I had got my 2012 case reviewed by renound tax consulting firm this year and they suggested that I should have filed 1040 NR for tax year 2012 because as per substantial presence test for 2012 I was a non-resident alien.

Not sure what to do now as amendment needs to be done but there is a confusion over the filing status now.

To amend this I need to file amended NR return and for that filing status needs to something other than married filing jointly.
But per IRS, once I have opted for married filing jointly I can't revert It to married filing separately.

Please assist.
 

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