gnomad-browser
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broadinstitute
Explore gnomAD datasets on the web
Just got caught by this--a CI run failed on `eslint`, which I'd have expected to be run by our pre-commit hooks but apparently isn't.
We have recently added snapshot integration tests, but the ones we have to date have fake data in them. For a more realistic test, we could capture real responses to...
See: https://github.com/broadinstitute/gnomad-browser/issues/928
Per discussion in https://github.com/broadinstitute/gnomad-browser/pull/935
Many components render differently based on the current dataset. Check for conditionals such as `datasetId.startsWith('gnomad_r3')`. Ideally, instead of checking the dataset ID directly, abstract checks into functions in [dataset-metadata](https://github.com/broadinstitute/gnomad-browser/tree/main/dataset-metadata). For...
Converting https://github.com/broadinstitute/gnomad-browser/issues/848 into a Zenhub epic. # Data pipeline ## Genes - [x] #858 - [x] #859 - [x] #1168 ## Coverage - [x] #1180 ## Variants - [x] #849...
Running the `genes` task fails `./deployctl data-pipeline run --cluster genes` Stack trace: ``` 2022-06-22 17:06:59,249 - gnomad_data_pipeline - INFO - Running prepare_gtex_v7_expression_data (Output does not exist) 2022-06-22 17:06:59 Hail: WARN:...
When starting a Dataproc cluster for the GRCh38 ClinVar data pipeline ([deploy/docs/UpdateClinvarVariants.md](https://github.com/broadinstitute/gnomad-browser/blob/main/deploy/docs/UpdateClinvarVariants.md)), use the same VEP init script and configuration as used to annotate v4.
See instructions in [reads/README.md](https://github.com/broadinstitute/gnomad-browser/tree/main/reads#adding-reads-for-a-dataset). Since v4 will use a different version of VEP than v3, the transcripts track in the IGV.js viewer will also need to be updated. - [reads/README.md#reference-data](https://github.com/broadinstitute/gnomad-browser/tree/main/reads#reference-data)...