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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

BaseRecalibrator Follow

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    prasundutta87

    Hi,

    There was a -bqsr option in old version of BaseRecalibrator. In order to produce a second recalibration table, you could give the first recalibration table to it along with the original BAM file and check through AnalyzeCovariates the difference in recalibration plots. It seems that it has been removed from GATK4 (don't know which specific version onwards). Is there a different workflow now to check the difference in the plots now? If yes, Can I be pointed to the correct documentation for it?

    Regards,

    Prasun

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    Bhanu Gandham

    Hi Prasun,

    Analyze Covariates is still part of GATK, here is the latest version: https://gatk.broadinstitute.org/hc/en-us/articles/360051304351-AnalyzeCovariates

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    prasundutta87

    Hi Bhanu,

    Thanks for your reply. Sorry, I was'nt clear with my question. I was going through some old documents on how to confirm if BQSR has worked well. In most of the documents, a second recalibration step was run using the BaseRecalibrator tool which made use of the -bqsr option where you could feed in the first recal table to get the second recal table which can be compared using AnalyzeCovariates.

    This option of -bqsr in BaseRecalibrator has been seem to have deprecated now and I did not find any document how to to perform the covariate comparison now as it has not been documented (atleast I did not find it). However, after doing some deep search, I got an answer from an old post in gatk GitHub page: https://github.com/broadinstitute/gatk/issues/322.

    Also, is it possible to get explainantions on the new graphs that gets produced using AnalyzeCovariates? Or can I please be pointed out to an appropriate documentation? I have seen the old one, but is there a new document?

    Regards,
    Prasun

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