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.
Is there a way to generate the BaseRecalibrator plots seen in the BQSRv2 presentation on the Dropbox. Specifically I am looking to plot the original qualities along with the recalibrated qualities so as to analyze the improvement after recalibration. With BQSRv1 this was done by running analyze covariates on the pre- and post-calibrated bam. So far I have only been able to get one sample plotted in the .grp.csv.pdf. Is there an argument for BaseRecalibrator that I am missing? Do I need to go in and work with Rscript directly?