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.
m2 gatk4 oncotated maf output includes rejected mutations
The oncotated maf output includes many rejected mutations (using the configuration from the public spaces). This is bad practice. The unfiltered VCF (or preferably a tsv) should have these sites but we should not be annotating them or putting them in final outputs.