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.
gatk 4.05 and "fix_misencoded_quality_scores"
Switching from gatk 3.8 to 4.05 to avail myself of '--enotype-filtered-alleles' I discovered a few format changes to familiar options.
But '--fix_misencoded_quality_scores' is no longer recognized.
My question is what does HC (gatk 4) do when it encounters the problems that were previously handled with the '--fix_misencoded_quality_scores' option?