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GenotypeGVCFs error; A USER ERROR has occurred: use-new-qual-calculator is not a recognized option

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    Samuel Terkper Ahuno

    i spotted where the error is coming from; it appears the work JointCalling workflow is not compliant with latest versions of gatk (4.1.6.0) and 4.1.5.0. and throws the error

    A USER ERROR has occurred: use-new-qual-calculator is not a recognized option

     

    However, it workflow runs when I maintain gatk version 4.1.4.0. 

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    Jason Cerrato

    Hi Sam,

    Have you made any modifications to the cloned workflow? The WDL shows that GATK ver 4.1.4.0 is being used for the workflow, and as such appears to be designed for use with this particular version of GATK. As you have discovered, this workflow works with 4.1.4.0 but not with 4.1.6.0 and 4.1.5.0. The methods team who developed this workflow has not created a version that works with GATK 4.1.5.0 or 4.1.6.0—as such, I would recommend running this workflow with 4.1.4.0.

    Kind regards,

    Jason

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