GATK-DRAGEN standalone pipeline?

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rcorbett

• January 07, 2022 21:45
• Edited

Hi folks,

I have been asked to try out your GATK-dragen pipeline.   I found this and related pages:

https://gatk.broadinstitute.org/hc/en-us/articles/4411716682011-Full-release-of-open-source-DRAGEN-GATK-1-0

And have been reading the docs to try and figure out if I can either:

1.) Get a list of the commands recommended to reproduce this pipeline on our system or

2.) Run the pipeline on my own system (ie. Not on Terra).    

I have downloaded the .wdl from here:

https://github.com/broadinstitute/warp/releases/download/WholeGenomeGermlineSingleSample_v3.0.0/

but am total newbie when it comes to .wdl.      Do you have any tips/tutorials/ideas about how I should go about testing the pipeline without having access to terra (or other cloud alternatives).   For example, where should I source the containers and references that are needed?

many thanks,

Richard

 

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  Genevieve Brandt (she/her)

  • January 10, 2022 17:04

  Hi rcorbett,

  This DRAGEN-GATK topic was just for the webinar in December, I am going to move your post into our Community Discussions -> General Discussion topic.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • January 11, 2022 18:49

  Hi rcorbett,

  The resources for the DRAGEN-GATK pipeline are all in our gs://gcp-public-data--broad-references/ google bucket. Here is the README where we describe the resources for this pipeline: https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/README_dragen_gatk_resources.txt

  Here is an overview of the main DRAGEN-GATK steps:

  1. Alignment with DRAGMAP using the masked reference file. https://github.com/Illumina/DRAGMAP
  2. In GATK, run CalibrateDragstrModel on your input bam. https://gatk.broadinstitute.org/hc/en-us/articles/4414602469531-CalibrateDragstrModel
  3. HaplotypeCaller per sample in DRAGEN mode using these arguments: --dragen-mode true --dragstr-params-path dragstr_model.txt

  We don't directly support WDL on this forum A good place for getting started with WDL is looking through the docs at https://openwdl.org and https://github.com/openwdl/learn-wdl. 

  Please let me know if you have any further questions!

  Genevieve

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  Genevieve Brandt (she/her)

  • January 13, 2022 20:14

  We have another helpful article I forgot about, which is a tutorial of the new DRAGEN-GATK steps: https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939

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  Abhay Rastogi

  • June 18, 2022 02:10

  Hi Genevieve,

  I'm aware that germine line variant calling can be performed in Dragen mode now. Can Dragen-GATK also be used with Mutect2 for somatic variant calling (tumor-normal samples)?

  It would be very helpful if you could link any webinars or tutorials which show how to run Dragen and Mutect2 on an HPC.

  Thanks,

  Abhay

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  Genevieve Brandt (she/her)

  • September 13, 2022 20:45

  Hi Abhay Rastogi,

  Thank you for posting your question to the forum! I'm sorry it took us so long to get back to you. 

  The DRAGEN-GATK options are only available in HaplotypeCaller. You can read more about this in another forum post here: https://gatk.broadinstitute.org/hc/en-us/community/posts/4411939432731-What-are-the-plans-for-expanding-DRAGEN-GATK-to-somatic-variants-

  Kind regards,

  Genevieve

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