gnomad-browser issues

Use gnomAD v4 variants for annotation in ClinVar data pipeline

ClinVar variants are annotated with gnomAD AC, etc. The ClinVar GRCh38 data pipeline currently uses gnomAD v3 for this. https://github.com/broadinstitute/gnomad-browser/blob/b4e38686e23fe4a31ff7c9541fe78b82b4df286b/data-pipeline/src/data_pipeline/pipelines/clinvar_grch38.py#L56-L65

nawatts

Component: Data Pipeline

Create data pipeline for v4 variants

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.

nawatts

Component: Data Pipeline

Update MANE Select transcripts

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

nawatts

Component: Data Pipeline

Update version of GENCODE used in genes data pipeline

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

nawatts

Component: Data Pipeline

Add primAD and genebass external links to variant page

1

WIP: https://github.com/broadinstitute/gnomad-browser/pull/890

mattsolo1

good first issue

GKE Upgrades blocked on due to use of deprecated APIs

1

It looks like our GKE cluster running gnomad won't auto-upgrade to the kubernetes 1.22 release, because some resources we have deployed are using deprecated APIs: Still have to track down...

sjahl

Component: Infrastructure

sre

Pin Hail version(s) used in data pipeline

We should pin the latest version of Hail used to successfully run data pipeline tasks. Could be in specified in [data-pipeline/requirements.txt](https://github.com/broadinstitute/gnomad-browser/blob/b497106d97773affd81b48eadfa5586259e011e5/data-pipeline/requirements.txt). However since some pipeline tasks are computationally intensive and...

mattsolo1

Component: Data Pipeline