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.
Normal-lod and tumor-lod in Mutect2
What are the normal-lod and tumor-lod in Mutect2?
What are the bases of the default values 2.2 and 3.0 respectively?
And, if the threshold are lowered or raised, what would be happened in terms of mutation calling?
Please, explain them by using very basic terms ( AD, AF, ...)