Update transcript mapping

genome-nexus / genome-nexus-importer

Import data into MongoDB for use by https://github.com/genome-nexus/genome-nexus/

MIT License

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Closed leexgh closed 2 years ago

leexgh commented 2 years ago

mskcc isoform overides has grch37 and grch38 version (https://github.com/mskcc/vcf2maf/tree/main/data), we should run for both and update our transcript mapping.
OncoKB sometimes use different transcript than msk_override, replace msk_override transcript to oncokb transcript
This pr also updates grch38_ensembl95 hgnc.

leexgh commented 2 years ago

Also I was having trouble updating grch38_ensembl95 hgnc (https://github.com/genome-nexus/genome-nexus-importer/pull/51), forget what was the error, but this time along with updating transcript mapping I found grch38_ensembl95 hgnc was updated successfully as well(https://github.com/genome-nexus/genome-nexus-importer/blob/26684c7f80fa1c331c65fc555e2b575efb28eb28/data/grch38_ensembl95/export/ensembl_biomart_canonical_transcripts_per_hgnc.txt), not sure why but this time it works without error

leexgh commented 2 years ago

Done - If oncokb transcripts differ from msk_overrides, we replace with oncokb transcript.