HOW to do a second pass to analyze after recalibration in GATK4

why the BaseRecalibrator function don't have -BQSR argument? I don't know how to do a second pass to analyze after recalibration in GATK4

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  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin
    edited January 7

    @dbecker

    Sorry about the delayed response.
    By second pass @wkyan do you mean the ApplyBQSR step?

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