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Old 05-17-2012, 09:57 AM   #1
ashkot
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Location: Cupertino, CA

Join Date: Nov 2011
Posts: 59
Default Issue with LiftOver

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
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Old 05-17-2012, 10:25 AM   #2
Heisman
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Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

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