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.
Effect of running BQSR per sample and not lane
What is the effect of running BQSR per sample across lanes and not per sample per lane i.e if @RG ID is per sample and not per sample lane. Does it introduce additional errors or just run BQSR sub-optimally? If So, how so?