Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz is suitble for WGS VQSR?
Answered
REQUIRED for all errors and issues:
a) GATK version used:GATK4.2.2
b) Exact command used: VariantRecalibrator --resource
c) Entire program log:
I noticed that the ExAC runner the VQSR with Axiom_Exome_Plus as knownsites. So, if running VQSR in WGS pipeline, should I applied the dataset as a knownsites too?
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Official comment
Hi lizhichao,
Thank you for writing into the GATK forum with your question! We have a resource regarding our recommendations for VQSR training and truth sets: https://gatk.broadinstitute.org/hc/en-us/articles/360035890831-Known-variants-Training-resources-Truth-sets.
Our GATK team is not the same team as the group that works on gnomAD or ExAC, so I don't have any specific recommendations regarding the file you listed. However, I can point you to our production pipelines usage of VQSR to see what we use as input parameters: https://app.terra.bio/#workspaces/warp-pipelines/Exome-Analysis-Pipeline.
The GATK resource bundle our team maintains is explained at this link: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle.
If you have any specific questions regarding the VQSR training and truth set article, our resource bundle, or the featured workspace, please let us know!
Best,
Genevieve
Comment actions -
Thank you for your post, lizhichao! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK.
We'll get back to you if we have any updates or follow up questions. Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi lizhichao,
We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!
Kind regards,
Genevieve
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