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Is there a 2nd pass base quality score recalibration in GATK4?
In the previous version of GATK, the base quality score recalibration process had an option to perform a 2nd pass that could be used in the "AnalyzeCovariates" step. While the GATK4 "AnalyzeCovariates" tool discussed the second pass, there is no specific options in the GATK4 "BaseRecalibrator" tool for performing a second pass. Please advise.