There is no parameter '-bqsr' in BaseRecalibrator of GATK version 4.beta.6 that could use to generate the 2nd recal table by include the 1st recal table.
Have a look at this thread. We will be sure to document this properly for the release
I have the same problem with GATK18.104.22.168. The parameter -bqsr, as indicated on slide 11 of the presentation "GATKwr21-03-Base_Recalibrator.pdf" for example, is missing in BaseRecalibrator. Is there a workaround to generate the 2nd recal table?
Sorry for the confusion. I will make sure the new slides (for the upcoming workshops) have the correct workflow/commands.
For now, I am quoting Soo Hee from the thread above. "BaseRecalibrator does not take the -bqsr parameter. To generate the 2nd recalibration table, you must use the recalibrated BAM with BaseRecalibrator."