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.
Indel realignment for MuTect2 in GATK 4.0
Hello I have already read that the indel realignment is deprecated in GATK 4.0, as HaplotypeCaller does the realignment, but what about MuTect2?
In one of your posts ( https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2 ) I see you already have data where indel realignment was done. Was this intentional?
How do I proceed with the pipeline then?
Should I run indel realignment on my data with 3.8 and then use 4.0 Mutect2?