Apply L2G pre-trained model to local GWAS data


I wonder if it is possible to download the pre-trained locus-to-gene (L2G) model and apply the gene prioritization scoring using local GWAS data? Any pointer would be greatly appreciated.


Hi @alhenry, and welcome to the Community! :partying_face:

The L2G pipeline step cannot be run in isolation, because some of the input data are created internally by the team using licensed data and therefore cannot be shared publicly.

This means that in order to run the L2G method on local GWAS data, you would need to spin up your own instance of Open Targets Genetics, and create your own input files. We are working towards making our pipelines easier to use, but they are not currently completely plug-and-play.