The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?