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.
How base-recalibrator deals with genuine biases in base quality?
Base quality may be genuinely associated with some covariates. For instance, average base quality may decrease at the end of the run; or average base quality may be genuinely different between the read groups that come from different runs. Will base quality recalibrator preserve the true quality differences in such cases?