gnomad-browser
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broadinstitute
Explore gnomAD datasets on the web
Replace references to v3 with updated information about v4 in [about](https://github.com/broadinstitute/gnomad-browser/tree/main/browser/about) and [help](https://github.com/broadinstitute/gnomad-browser/tree/main/browser/help) content.
When a specific version/subset is included, the URL includes the gnomAD version. For example: - v2 https://gnomad.broadinstitute.org/variant/1-55516888-G-GA?dataset=gnomad_r2_1 - v3 https://gnomad.broadinstitute.org/variant/1-55051215-G-GA?dataset=gnomad_r3 Once gnomAD v4 is released, v3 will no longer be...
Add sample counts, overall age distribution, quality metric distributions, etc. for v4 to [dataset-metadata](https://github.com/broadinstitute/gnomad-browser/tree/main/dataset-metadata).
Since v4 includes exomes, update the default dataset shown in the browser to v4. https://github.com/broadinstitute/gnomad-browser/blob/b4e38686e23fe4a31ff7c9541fe78b82b4df286b/browser/src/Routes.js#L34
Update the list of available datasets / subsets in the [dataset menu](https://github.com/broadinstitute/gnomad-browser/blob/main/browser/src/DatasetSelector.js).
API requests for STRs and mitochondrial variants currently use a v3 dataset ID. Should they be changed to v4?
If v4 adds new fields to variant data (such as a combined FAF for exomes/genomes), extend the [variant GraphQL schema](https://github.com/broadinstitute/gnomad-browser/blob/main/graphql-api/src/graphql/types/variant.graphql) to include them. Ensure that these fields are compatible with...
Add v4 as an option for dataset arguments. - [graphql-api/src/graphql/types/dataset-id.graphql](https://github.com/broadinstitute/gnomad-browser/blob/main/graphql-api/src/graphql/types/dataset-id.graphql) - [graphql-api/src/datasets.js](https://github.com/broadinstitute/gnomad-browser/blob/main/graphql-api/src/datasets.js) Add GraphQL queries for v4 variants. - [graphql-api/src/queries/variant-datasets](https://github.com/broadinstitute/gnomad-browser/tree/main/graphql-api/src/queries/variant-datasets) - [graphql-api/src/queries/variant-queries.js](https://github.com/broadinstitute/gnomad-browser/blob/main/graphql-api/src/queries/variant-queries.js)
Currently, lifted over v2 variants are annotated based on their presence in gnomAD v3. https://github.com/broadinstitute/gnomad-browser/blob/248432d6b9658938eba6bc25638820f07327db1e/data-pipeline/src/data_pipeline/pipelines/liftover.py#L53-L60 That needs to be updated to use gnomAD v4.
Add configuration to the [export_to_elasticsearch](https://github.com/broadinstitute/gnomad-browser/blob/main/data-pipeline/src/data_pipeline/pipelines/export_to_elasticsearch.py) pipeline and load v4 variants into Elasticsearch.