I was wondering how can i download the list of GWAS data and annotations that are used in Open Targets… For example i would like to have a list with start- stop positions , GWAS/rs ID, gene ID a pvalue and information about functional annotations (enhancers, promoters etc). I checked the open-targets-genetics google storage and there are some files is this correct ? Should I download the v2g and l2g directories ? How can I visualize those spited parquet files in the particular directories in one table ?
Do you know any other way to find and download these data ?
Hi @Dimitris_Zisis and welcome to our Community!
Sorry for the late reply. We are working towards a better documentation of our datasets, so that the available data and its metadata is more transparent to our users. For the time being, let me point you to the datasets you might find of interest:
- For variant related information and functional annotation(genomic coordinates, rsID), you wanna look at our variant index: Index of /pub/databases/opentargets/genetics/latest/lut/variant-index
- For variants associated with traits and their association signals, go to variant-to-disease: Index of /pub/databases/opentargets/genetics/latest/v2d
- V2G and L2G are datasets that establish relationships between any variant and its related genes (V2G), or loci and their likely causal genes (L2G). L2G is based on V2G information.
You’ll find a more comprehensive explanation of our data and pipelines in our docs.
Best,
Irene
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