ApplyBQSR - first and second pass re-calibration tables

I am following this run BQSR documentation which suggested generating first and second pass recalibration tables and analyze through AnalyzeCovariates .

In GATK4, ApplyBQSR replaces this functionality and outputs a recalibrated BAM file. How do we generate the second pass table with ApplyBQSR?
Do you have any documentation for interpretation of plot results generated thorugh AnalyzeCovariates ?


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    Accepted Answer


    Have a look at this thread. We don't have any specific documentation for AnalyzeCovariates, but the article at the beginning of that thread may help, as well as doing a search for "AnalyzeCovariates" in the forum.


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