Question: Does Unified Genotyper use any minimum and/or maximum read depth to call variants?
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gravatar for apeiravan
3 months ago by
apeiravan0
apeiravan0 wrote:

Hi I am using GATK beta, and calling SNPs with Unified Genotyper (Unified Genotyper SNP and indel caller (Galaxy Version 0.0.6)) followed by variant recalibration. I did not see any minimum depth filter recommended in the GATK best practices, but it seems like i should be filtering for depth after VQSR?

Thanks, Ati

snp • 128 views
ADD COMMENTlink written 3 months ago by apeiravan0
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