Nick Watts
Nick Watts
Create a [data pipeline](https://github.com/broadinstitute/gnomad-browser/tree/main/data-pipeline/src/data_pipeline) for gnomAD v4 variants. Much of the [v3 pipeline](https://github.com/broadinstitute/gnomad-browser/blob/main/data-pipeline/src/data_pipeline/datasets/gnomad_v3/gnomad_v3_variants.py) can probably be reused, but exome data will need to be added and joined to genome data.
Check if a newer version of [MANE Select](https://www.ncbi.nlm.nih.gov/refseq/MANE/) transcripts are available and if so, update the version used in the genes data pipeline. https://github.com/broadinstitute/gnomad-browser/blob/b4e38686e23fe4a31ff7c9541fe78b82b4df286b/data-pipeline/src/data_pipeline/pipelines/genes.py#L82-L84
Update the version of GENCODE used in the genes data pipeline to match the version used in the version of VEP used to annotate v4. https://github.com/broadinstitute/gnomad-browser/blob/b4e38686e23fe4a31ff7c9541fe78b82b4df286b/data-pipeline/src/data_pipeline/pipelines/genes.py#L36-L38
Reload variant data after changes to data pipeline in #862, #863, #864, and #865.
These settings affect how quickly shards transfer from temporary loading nodes to persistent data nodes. https://www.elastic.co/guide/en/elasticsearch/reference/6.8/shards-allocation.html https://www.elastic.co/guide/en/elasticsearch/reference/6.8/recovery.html
Currently, gnomAD can only be browsed by Ensembl genes / transcripts. It should also support RefSeq genes / transcripts. This only applies to gnomAD v3.1+. This requires VEP annotations with...
A few less than ideal things in demo deployments: * IP addresses in browser logs are wrong because the demo ingress IP isn't included in real IP config * API...
Some queries validate gene/transcript IDs as "ENSG###" / "ENST###".
Currently, transcript annotations may be annotated with `refseq_id` / `refseq_version` fields. https://github.com/broadinstitute/gnomad-browser/blob/b4e38686e23fe4a31ff7c9541fe78b82b4df286b/data-pipeline/src/data_pipeline/data_types/variant/transcript_consequence/annotate_transcript_consequences.py#L84-L120 The original intent here was to show both Ensembl and RefSeq IDs for MANE Select transcripts. However, most...