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.
How to optimise parameters for sequencing at higher depths?
I have a targeted bait panel that covers approximately 350Kb, our plans are to sequence tumour libraries to approximately 1200x post deduplication, we do not have a matched normal. The high depth is in order to detect rare variants.
Do you have any advice on which parameters within Mutect2 (tumour-only mode) and FilterMutectCalls that should be tweaked not only to take into account the lack of a matched normal but also the extreme depth of sequencing?
Any advice would be greatly appreciated.