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?

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?

1

I executed BaseRecalibrator on my .bam and obtained a Recalibration_data.table file. Now, When I apply PrintReads, the option -BQSR is not acknowlegded 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!


BaseRecalibrator


-BQSR


printreads

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