If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
Do we need to implement baseRecalibration before creating Panel of Normal?
I am wondering if I need to perform base recalibration on the normal bam files before I proceed with creating the panel of normals, which will then be used for somatic mutation calling with MuTect2.
The tutorial (https://software.broadinstitute.org/gatk/documentation/article?id=11136) and the documentation (https://software.broadinstitute.org/gatk/documentation/article?id=11127) suggest to me that baseRecalibration is not required, but I wanted to confirm before proceeding with the pipeline.