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Variant Nomenclature mapping to OMOP Genomic vocab variants

We are starting to look at mapping variant details to the OMOP genomic vocabulary. The source data includes variations using a nomenclature system like the one described in Nomenclature for the description of sequence variations (mutation nomenclature) and would like to map them to the genomic vocabulary. Usagi isn’t particularly useful in terms of picking up the matches and so thought it may be useful to parse these into text that is similar to that which is contained within the genomic vocab which may give us more hits with usagi or atleast closer matches. Is this the direction we should be heading in and if so does anyone know if there are any tools available or that are being worked on?

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Hello @tomstone786

My colleagues and I are currently working on a tool that maps genomic variants to OMOP Genomic. The beta version can be found via this link: koios.ohdsi.org/

Do you think this is something that you could use here? It works for most formats of VCF files, as well as for TXT/CSV files with HGVSs.

Hi @nadia resurrecting this question after some time in the wilderness. Are there any details on using it with txt/csv files and the format they need to be in. Took a look at the repo and couldn’t see much detail around that side of things are those file types still supported?

Main challenge is how we link hgnc ids with the vocabularies.