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 Empty vcf file even with tumor/normal pair input
Hi I am aware of a bug in MuTect2 that gives an empty vcf file when generating PON. However I am experiencing the same issue when using tumor/normal pair mode as well. The log file indicates a "Ran local assembly on 0 active regions" error. The only different aspect of my dataset is that I am looking at only 3 amplicons on three different locations in human. Does this have an impact of how MuTect2 works?