Issue with LiftOver

[ashkot]

Hi all,
I have a lot if variants (more than 30K) with HG18 coordinates and i wanted HG19 coordinates for each one of them.

Aware that this can be done using liftover, the problem is i have to input as chr1:123-1234 (for e.g), i tried in BED format and it keeps giving an error.

The issue is i don't have any way to put an identifier on the returned data. So when i am parsing the output i want to be a 100% sure about updating my database.

Any ideas how this can be done?

Thanks,
Ashwin

[Heisman]

I don't understand your problem? What error did it give? Could you post a couple of input lines?