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Old 07-26-2011, 06:36 AM   #1
jorge
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Default QC in GATK VCF output

Hello,

I've run GATK to call SNPs and got the corresponding VCF output. Now I'm wondering if there are some pre-established cut-offs for the phred, depth quality, etc that I could use to discard false positives.

any help will be welcome.

Tahnks
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Old 07-26-2011, 08:51 AM   #2
RDW
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Default

The GATK wiki describes some basic cutoffs you could use ('hard filtering'):

http://www.broadinstitute.org/gsa/wi...hard_filtering

However, they now have a more sophisticated approach ('Variant quality score recalibration'):

http://www.broadinstitute.org/gsa/wi..._recalibration
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Old 07-26-2011, 10:34 PM   #3
jorge
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Thanks

that was of great help.

Jorge
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