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BaseRecalibrator Plots

atbrightatbright Member
edited September 2012 in Ask the GATK team

Is there a way to generate the BaseRecalibrator plots seen in the BQSRv2 presentation on the Dropbox. Specifically I am looking to plot the original qualities along with the recalibrated qualities so as to analyze the improvement after recalibration. With BQSRv1 this was done by running analyze covariates on the pre- and post-calibrated bam. So far I have only been able to get one sample plotted in the .grp.csv.pdf. Is there an argument for BaseRecalibrator that I am missing? Do I need to go in and work with Rscript directly?

Best Answer

  • rpoplinrpoplin ✭✭✭
    edited September 2012 Accepted Answer

    Hi there,

    The workflow for generating the plots is basically the same as before but has been streamlined since CountCovariates and AnalyzeCovariates were combined together when we made BaseRecalibrator.

    It works something like this:

    Your original recalibration job produces a recalibration table (-o recal_data.grp) and plots showing the pre-recalibration accuracy.

    Now run the BaseRecalibrator again using the original bam and passing in the recalibration table you just generated (-BQSR recal_data.grp). This additional argument tells the GATK-engine to actually perform the recalibration. The output will be a pdf showing both the pre- and post- recalibration accuracy on the same plots.

    Cheers,

Answers

  • rpoplinrpoplin Member ✭✭✭
    edited September 2012 Accepted Answer

    Hi there,

    The workflow for generating the plots is basically the same as before but has been streamlined since CountCovariates and AnalyzeCovariates were combined together when we made BaseRecalibrator.

    It works something like this:

    Your original recalibration job produces a recalibration table (-o recal_data.grp) and plots showing the pre-recalibration accuracy.

    Now run the BaseRecalibrator again using the original bam and passing in the recalibration table you just generated (-BQSR recal_data.grp). This additional argument tells the GATK-engine to actually perform the recalibration. The output will be a pdf showing both the pre- and post- recalibration accuracy on the same plots.

    Cheers,

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