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Whats the Reseaon for using GATK4-BQSR in your PublicPairedSingleSampleWf

EADGEADG KielMember ✭✭✭

Hi Folks,

is there any benefit from using the GATK4-Version of BQSR ? Harder, Better, Faster, Stronger ?;)


Best Answer


  • EADGEADG KielMember ✭✭✭

    Thanks @Geraldine_VdAuwera, this Spark-Version sounds pretty nice :). Will we get an updated PublicPairedSingleSampleWf e.g. Docker with the GATK 4 release ?

    Issue · Github
    by Sheila

    Issue Number
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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @EADG, to be clear the current PublicPairedSingleSampleWf points to the latest Docker we use in production, which includes an alpha of GATK4 and is shared publicly on Dockerhub. And to answer a very frequently asked question up front, yes, we are already using a few components of the GATK4 alpha in production. The overall GATK4 package is still considered alpha because it is not feature-complete (you can't run the full germline short variant discovery pipeline with it) but some components have been deemed fully equivalent (in terms of results) to their GATK3 counterparts and therefore ok to use in production. The WDL script we share reflects that judgment. And of course we'll update the shared WDLs and corresponding docker image when we update our prod pipeline.

    The Spark versions of the tools aren't used in production yet; we plan to do some evaluations to see what level of "sparkification" gives us the best bang for our buck. When we know, we'll let you know :)

    Note that we do plan to release Docker images of every GATK release; we'll do that for all 3.x versions, and for 4.x starting with 4.0. These will be generic images with just GATK and what it needs, independently of the pipeline Dockers, which includes everything that's need in the pipeline. We hear that people want either one or the other depending on their use cases, and we want to be sure to satisfy those needs.

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