Question: Does Unified Genotyper use any minimum and/or maximum read depth to call variants?
gravatar for apeiravan
9 months ago by
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 • 279 views
ADD COMMENTlink written 9 months ago by apeiravan0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 94 users visited in the last hour