Entering edit mode
5.4 years ago
ste.lu
▴
80
Hi All,
Are you aware of a database or a way to help me in this task: Given a set of ~100 GWAS, how can I collect all the lead and tag SNPs called in these studies and merge them in a big tsv?
What I've done so far was download from EBI GWAS catalog all the GWAS I am interestes in. In this file I have info only on the papers and there is a unique code (e.g.: GCST004599) which redirect to the Open Targets Genetics DB.
I've been trying to recall the variants from the study ID in this DB but no luck so far. They are using a api + graphql structure. The query structure is this. there is no way, to me, to connect StudyID to VariationID.
Did anyone had a similar problem? or can suggest any solutions?
Get SNPids, and use 1000Genome data to get tag SNPs at LD>0.9(?) ?
But how can I select the SNPs for a trait?
The GWAS catalog would have a column saying which trait, use that to filter out?
What file did you download from the GWAS Catalog? From what I can see both the studies and association files will give you all the associated variants, already in a TSV. You just need to filter the file to only show you the studies you're interested in.