I executed BaseRecalibrator on my bam and obtained a Recalibration_data.table file. Now, When I apply PrintReads, the option
-BQSR is not acknowledged by PrintReads. Even online or in the list of arguments there is nothing I can relate to this, the how does PrintReads apply the recalibration if I don't provide this file?
Keep in mind I'm very new in the bioinformatics field. Thanks a lot!