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ClinVar is an external data source that aggregates and curates information about the impacts variants have. Their dataset updates frequently, and the gnomAD browser aims to keep the ClinVar informatio…
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- Dockerfile
- cloudbuild
- script to deploy cloud run job (e.g. deploy-job.sh from `clinvar-ingest`)
- github action to run the deploy-job.sh on main merges or maybe on releases like `clinvar-inge…
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Dear ClinVar API Submitter,
Thank you for using the ClinVar Submission API! We are making changes to the API submission schema to support classifications of somatic variants. The details of the prop…
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Hi all, thanks for developing this very useful tool.
I have a question on how the clinvar variant significance annotation table is matched to the generated guides. I've attached a subset of my out…
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For variants included in preliminary estimates, we should be removing any HC pLoF variant that has a clinvar classification of Benign or Likely Benign. I thought we had already done that but this ex…
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Do you have code used to make the tidy clinvar file? I'd like to update this as it looks like it was last update over a year ago.
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Dear Prof. Wang!
I try to update to ANNOVAR, but it gives error:
```
Error: invalid record found in avinputfile: A;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=TNFRSF14:8764|TNFRS…
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We currently load ClinVar from separate GRCh37/38 VCFs
We should switch to the XML as it contains more variants and more info.
For analysis performance reasons we probably need it to continue to go …
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Add Q/A measures to per ClinVar release ingest. Measures include:
- count of VCVs, SCVs, RCVs, Genes, Submitters, Submissions, etc. pcregrep'd from XML file
- compare those to counts from BQ tables
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GitHub repo: https://github.com/ncbi/clinvar/tree/master/submission_api_schema
Test endpoint: https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions
Submission API documentation: https://www.ncbi.…