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 4.4 PrintReads "BQSR is not a recognized option"
I'm trying to perform base recalibration using GATK 4.4 docker image but PrintReads is crashing with the following error: "BQSR is not a recognized option". I tried -bqsr, -BQSR, --bqsr and --BQSR, since the online documentation is outdated and the local doc does not mention any "bqsr" option, it is very unclear how to use that tool or even if it actually still exists in the latest version.
what am I missing to perform that step as described in the GATK best practices?