How do I specify the Recalibration_data.table for "PrintReads" in GATK 4.3, if the tool does not admit -BQSR as an option anymore?

Question

[javiflaja]

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!

Answer 1

[Pierre Lindenbaum]

do you want ApplyBQSR "Apply base quality score recalibration " ? https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR