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.
Base recalibration & realignment without known sites
Dear GATK team,
Thanks a lot for the new GATK version and GATK forum!
I am trying to use GATK for yeast strains. I do not have files of known sites of SNPs/indels.
I understand that the BaseRecalibrator must get such a file.
Do you suggest to skip calibration and realignment, or is there another way to go here?