if i worked a half year in 2012 and they put me on self emplyment the next 6 months?

if this was the same job for all the time you worked there, it is not legal to give you a W-2 and 1099 for the same job

having said that, you don't have much choice at this point to file your tax return claiming the W-2 as wages on Line #7 and the 1099 on Sch C and SE, and yes you will likely owe self employment tax and since you haven't paid your anticipated taxes on 1040ES for at least two quarters, you will likely owe money, and possibly underpayment penalty

you might want to get an SS8 from www.irs.gov, complete it and submit to IRS for their determination as to what your status is

As long as your tax paid in is equal to or greater than the tax you owed last year you can use exception 1 and there is no penalty. If not you are subject to penalty.

What do you mean they put you on self employment. An employer can't change an employee to an independent contractor when the job doesn't change and it doesn't matter if you consented. File IRS Form SS-8 http://www.irs.gov/pub/irs-pdf/fss8.pdf to get an official ruling that you are an employee

If you owe more than $1000, there is a penalty.

Who put you on self employment? that makes no sense.