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.
Use TCGA variants instead of COSMIC
I am wondering about the possibility to use TCGA variants instead of cosmic in MuTect. Given that it's mostly used to upweight positions that are in dbSNP AND cosmic I think this would be a smart move. Cosmic seems like a mess, with small single-gene experiments mixed with larger experiments. The TCGA pancan MAF seems way mor structured. My guess is that most dbSNP somatic variants are so common that they will be in TCGA pancan as well.
Has anyone tested this or have experience with it?
(my basic plan is to convert TCGA pancan MAF to VCF and use in MuTect).