Question: Does Unified Genotyper use any minimum and/or maximum read depth to call variants?
gravatar for apeiravan
15 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 • 457 views
ADD COMMENTlink written 15 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: 172 users visited in the last hour