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broadinstitute / variant-curation-portal

Web application for curating loss of function variants
https://lof.curation.broadinstitute.org
MIT License
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update script for pulling variants to deal with refseq variants #227

Closed msingerb closed 3 years ago

msingerb commented 3 years ago

Since the hail table now has the refseq annotations as well I think for now we want to exclude these annotations from future projects and only curate those that are visible in the browser as Lof. This means we only want annotations of LoF variants in ensembl transcripts.

nawatts commented 3 years ago

The script in this repository filters transcript consequences based on the provided gene IDs. So as long as Ensembl gene IDs are given, it would not include consequences for RefSeq transcripts.

https://github.com/macarthur-lab/variant-curation-portal/blob/2a466c9437b3eb45e42422fb72e6577c4131bbc8/scripts/get_gnomad_lof_variants.py#L162-L170

Based on Slack messages, my best guess is that variants for some projects were pulled using a different version of the script that filtered by gene symbol instead of ID. That would include both Ensembl and RefSeq consequences, since they both have the same gene symbols.