Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Criteria for filtering OxoG artifacts in Mutect2
What filter criteria should one apply to filter out OxoG artifacts for M2 calls?
Elsewhere in the forum, it is mentioned that "You can use the FOXOG annotation as an estimate of whether the relative support from the two pair orientations indicates bias or not." If this the annotation is to be used for filtering, what is the threshold that to filter out calls that show a bias.
Thanks for your input!