Nick Watts

Currently, the MANE Select transcripts pipeline keys its output table by Ensembl gene ID. https://github.com/broadinstitute/gnomad-browser/blob/b4e38686e23fe4a31ff7c9541fe78b82b4df286b/data-pipeline/src/data_pipeline/data_types/mane_select_transcript.py#L16-L25 Also, the annotate_transcript_consequences function only checks the annotation's transcript ID against the MANE Select transcript's...

VEP annotations for Ensembl transcripts do not include version numbers, whereas annotations for RefSeq transcripts do. For RefSeq transcripts, the version number needs to be removed when collecting canonical transcripts...

VEP annotations for Ensembl transcripts do not include version numbers. Thus, version numbers are annotated using data from the version of GENCODE used by VEP (from the output of the...

The ranking of VEP consequences in the browser does not match Ensembl's ranking. https://github.com/broadinstitute/gnomad-browser/blob/8fdd162ae3248b736df8e87dd43bbb402ca2cf4a/browser/src/vepConsequences.js#L1-L182 https://ensembl.org/info/genome/variation/prediction/predicted_data.html#consequence_type_table Not sure why. The browser's ranking seems to have been that way since ranking was...

Currently, creating a deployment using `deployctl` creates a local kustomization.yaml file and applying the deployment applies it using `kubectl`. https://github.com/broadinstitute/gnomad-browser/blob/95f5d24f540f8132dc9cf546226ae9581bb095bb/deploy/deployctl/subcommands/browser_deployments.py#L31-L35 However, the only thing that changes is the image tag...

The dataset menu shows the selected version of gnomAD and the number of samples in the dataset.  However, it always shows information...

Use GA4GH VRS identifier as Elasticsearch document ID for variants?

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To avoid the possibility of indexing multiple copies of a document in Elasticsearch, each document must have a unique ID. Currently, the document ID used for variants is a compressed...

Use Kustomize to manage K8S deployments

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Currently, K8S deployments are managed using [manifests](https://github.com/broadinstitute/gnomad-browser/tree/main/deploy/manifests) and custom wrappers around kubectl ([deployctl](https://github.com/broadinstitute/gnomad-browser/tree/main/deploy/deployctl)). These should be replaced with Helm. (EDIT: Adding a checklist) - [x] https://github.com/broadinstitute/gnomad-deployments/pull/1 - [x] https://github.com/broadinstitute/gnomad-deployments/pull/2 -...

Currently, cloud infrastructure for the browser is managed using gcloud or the Cloud Console and changes manually added to a Python script that sets up everything from scratch ([deploy/deployctl/subcommands/setup.py](https://github.com/broadinstitute/gnomad-browser/blob/efcee6869093bd45a10309e522d80498e88f277e/deploy/deployctl/subcommands/setup.py)). Instead,...