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.
RNA-seq and WGS for cancer samples (no paired T-N)
Dear GATK Team,
I want to do SNP calling on cancer RNA-seq data (no matching normals). In some cases I have matching WGS data (for which I also want to do SNP calling) - but not for most cases.
If I understood this correctly I cannot use MuTect2 without matching normals - so do you then recommend GATK or a completely different tool?
I very much appreciate your help.