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Old 08-27-2012, 09:49 AM   #1
manducasexta
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Location: San Francisco

Join Date: Mar 2009
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Default strategy to convert low GQ calls to "no call"

Hi all -

I have a VCF file containing genotypes for 12 samples at variant positions only. I'd like to convert those genotypes with GQ scores under a threshold to "no call" (i.e. ./.)

Does anyone know a utility to do this? My best thought at this point is to script it myself.

Thanks in advance!
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