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Error when trying to generate the second recalibration table for AnalyzeCovariates

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    Genevieve Brandt (she/her)

    Hi ISmolicz,

    I looked through all of our GATK4 tool docs and could not find any mention of this option. The only information I could find was on our legacy site with much older versions of GATK that we do not support anymore.

    However, I don't think you need that option to run AnalyzeCovariates. You should be able to input any recalibration table to get the plots.

    Best,

    Genevieve

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    ISmolicz

    Thank you for your reply Genevieve Brandt.

    I would like to submit both a first and second pass recalibration table to AnalyzeCovariates. If the option mentioned above is unavailable, how can the second pass recalibration table be generated? Is it by running BaseRecalibrator on a BAM that has already been recalibrated once with BaseRecalibrator and ApplyBQSR?

    Thank you again.

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    Genevieve Brandt (she/her)

    Hi ISmolicz,

    I was able to find information about the first and second pass recalibration on our legacy site. I'll rephrase it here so people can more easily find it:

    Base Recalibration has two steps in GATK4:

    1) First pass of the base quality score recalibration. Generates a recalibration table based on various covariates. The default covariates are read group, reported quality score, machine cycle, and nucleotide context. For more info: https://gatk.broadinstitute.org/hc/en-us/articles/360050815072-BaseRecalibrator 
    2) Second pass or the second steps is the Apply base quality score recalibration. This tool performs the second pass in a two-stage process called Base Quality Score Recalibration (BQSR). Specifically, it recalibrates the base qualities of the input reads based on the recalibration table produced by the BaseRecalibrator tool, and outputs a recalibrated BAM or CRAM file.

    So, the second pass is the ApplyBQSR step.

    For more info please take a look at this detailed document: https://software.broadinstitute.org/gatk/documentation/article?id=11081

    Best,

    Genevieve

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    ISmolicz

    Hi Genevieve Brandt,

    Thank you for your reply and for the additional information.

    AnalyzeCovariates allows one to submit more than one recalibration table and states:

    Second pass recalibration tables results from the application of org.broadinstitute.hellbender.transformers.BQSRReadTransformer on the alignment recalibrated using the first pass tables.

    ApplyBQSR does not generate a second recalibration table and therefore, how can the second pass recalibration table be generated using a tool from the Tool Index? What would be the equivalent tool for BQSRReadTransformer?

    I would like to compare BQSR tables pre- and post-recalibration, similar to what is described in the following video, although I understand this describes GATK4-beta: https://www.youtube.com/watch?v=Zd58XBlBFk4

    Thank you again for your time and help.

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    Genevieve Brandt (she/her)

    Hi ISmolicz

    We no longer support GATK3 or GATK4 Beta, so unfortunately I do not have any other information regarding this question. You can look more on our legacy forum site for information about older versions of GATK.

    Thank you,

    Genevieve

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    ISmolicz

    Hi Genevieve Brandt,

    Thank you for your reply.

    I am a little confused as AnalyzeCovariates GATK v4.1.9.0 says that it can accept a -before and -after recalibration table and discussed a second pass recalibration table. Is this instead not the case and a post-recalibration table cannot be generated to compare to pre-recalibration?

    Thank you again.

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    Genevieve Brandt (she/her)

    I will put in a documentation request for my team to update the AnalyzeCovariates documentation. I agree, it does not make sense with the current BQSR method. I will try to get clarity to determine what the recommended method is for GATK4 and get back to you.

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    ISmolicz

    Thank you Genevieve Brandt - I am grateful for your help.

    I look forward to your reply.

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    Genevieve Brandt (she/her)

    Hi ISmolicz,

    We did not have an easy solution to this request and so I have created a ticket where our team will discuss the GATK4 method. You can follow along here: https://github.com/broadinstitute/gatk/issues/7096

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    ISmolicz

    Hi Genevieve Brandt,

    Thank you for letting me know and for setting up this ticket. I will ensure I check the relevant page for updates.

    Kind regards.

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