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.
Mutect2 PON with one normal sample
I am trying to analyze several tumors and one normal with mutect2. They are not paired. Is it appropriate to use -I normal ? or create pon with one normal sample and use -pon option? Tried to use mutect2 tumor-only mode to call the normal sample and use CreateSomaticPanelOfNormals, the result is an empty vcf with only headers. Any suggestions would be appreciated.