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VariantRecalibrator plot?

brdidobrdido São Paulo - BrazilMember

HI again!

Could you please help me to generate the first plot in the attached file which refers to VariantRecalibrator?

In other words, is this plot generated at the same time as my_sample.bqrecal.vqsr.R.scripts.pdf? If so, maybe some R library is missing but i can't find anything wrong in the log files (my_sample.bqrecal.vqsr.R.scripts.pdf seems to me fine adn healthy).

Thanks in advance,

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    H Rodrigo,

    It sounds like your setup is fine if you're getting a pdf generated. Can you please post your command line, and also attach the pdf file called my_sample.bqrecal.vqsr.R.scripts.pdf ?

  • brdidobrdido São Paulo - BrazilMember
    edited June 2013
  • brdidobrdido São Paulo - BrazilMember

    Humm, thanks again Geraldine. But that plot was so cool. lol

    See ya

  • splaisansplaisan Leuven / Gent (Belgium)Member

    Hi Geraldine,
    About the beautiful plots generated by the re-calibrators. Is there some tutorial on how to interpret them.
    I would like to be able to comment on these plots instead of just admiring their colourfulness.
    Thanks in advance.

    plots from:

    • AnalyzeCovariates
    • recalibrate_SNP_plots.R
    • recalibrate_INDEL_plots.R

    I found this sentence but no link (yet). For detailed instructions on how to interpret these plots, please refer to the online GATK documentation


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Man, you're everywhere today :)

    For the base recalibration plots, we don't currently have an interpretation tutorial, so for now the best way to get a detailed explanation of how they work/what they show is to watch the workshop video, which you can find linked in the Best Practices or on the Events page.

  • splaisansplaisan Leuven / Gent (Belgium)Member

    The reason is I finally decided to learn how to use your magnificent toolbox. I spent a week on it but I am rewarded now and want to learn more.

    I just did follow the 2013 score re-calibration video #5 and it was enlightening indeed. I need some more practice to understand the 'nuances' though.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Glad to hear you're liking it :)

    GATK has a non-trivial learning curve, but it is very powerful once you get to know it well. Documenting it is a non-trivial piece of work too of course, and it's still a work in progress!

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