Error: GATK Terra HaplotypeCaller Workflow

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Linda Do

• January 05, 2021 00:03

Hello!

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: Terra

I am trying to use https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- from Best Practices.

I used the Terra link from "Generic germline short variant per-sample calling" (https://app.terra.bio/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-hg38) and then wanted to look at the workflow called "2-Haplotypecaller-GVCF". But then an error message pops up saying "Error loading data". And at the top of the page is "You do not have access to this workflow, or this snapshot has been removed. To use this workflow, contact the owner to request access, or select another snapshot."

Is there a way to look at and use this workflow?

Thank you in advance.

 

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  Samantha (she/her)

  • January 06, 2021 15:35

  Hi Linda Do,

   

  Thanks for writing in. The 2-Haplotypecaller-GVCF workflow in the Germline-SNPs-Indels-GATK4-hg38 workspace is unpublished because it is outdated. You can instead use the Haplotypecaller workflow from the GATK4-Germline-Preprocessing-VariantCalling-JointCalling workspace.

  Please let me know if you have any other questions.

   

  Best,

  Samantha

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  Linda Do

  • March 15, 2021 05:15

  Thank you! That workspace was very helpful!

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