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.
About panel-of-normals, I understood that it is not essential but it is better to use it. Is there a standard panel of normals (PON) file been created for GATK4 mutect2 like for germline-resource (ftp://[email protected]/bundle/Mutect2/)? I tried to create a PON from my samples (3 normal samples), but in step 2 - Create a GenomicDB too many files were opened (I stopped it when about 50,000 files were opened). How many files are opened in this step and in addition, is it OK to create a PON from only 3 samples?