Question: Does Unified Genotyper use any minimum and/or maximum read depth to call variants?
0
apeiravan • 0 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