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.
SNP and INDEL VariantFiltration Parameters
I've been looking for recommended filter expressions for SNP and INDEL variant filtration. I found these articles on the topic: one and two. I noticed that in the second article the SOR annotation is recommended for both SNP and INDEL filtration, while in the first article it is not. I would like to know which of these filter expressions would be considered Best Practice for variant filtration.