gnomad-browser
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broadinstitute
Explore gnomAD datasets on the web
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...
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...