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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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Missing parameter '-bqsr' in BaseRecalibrator of GATK version 4.beta.6

There is no parameter '-bqsr' in BaseRecalibrator of GATK version 4.beta.6 that could use to generate the 2nd recal table by include the 1st recal table.


  • SheilaSheila Broad InstituteMember, Broadie admin


    Have a look at this thread. We will be sure to document this properly for the release :smile:


  • Hi,
    I have the same problem with GATK4.0.0.0. The parameter -bqsr, as indicated on slide 11 of the presentation "GATKwr21-03-Base_Recalibrator.pdf" for example, is missing in BaseRecalibrator. Is there a workaround to generate the 2nd recal table?


  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Stefan,

    Sorry for the confusion. I will make sure the new slides (for the upcoming workshops) have the correct workflow/commands.

    For now, I am quoting Soo Hee from the thread above. "BaseRecalibrator does not take the -bqsr parameter. To generate the 2nd recalibration table, you must use the recalibrated BAM with BaseRecalibrator."


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