Question: from GWAS to variants
0
gravatar for ste.lu
4 months ago by
ste.lu40
ste.lu40 wrote:

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?

snp gwas • 203 views
ADD COMMENTlink written 4 months ago by ste.lu40

Get SNPids, and use 1000Genome data to get tag SNPs at LD>0.9(?) ?

ADD REPLYlink written 4 months ago by zx87547.1k

But how can I select the SNPs for a trait?

ADD REPLYlink written 4 months ago by ste.lu40

The GWAS catalog would have a column saying which trait, use that to filter out?

ADD REPLYlink written 4 months ago by zx87547.1k

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.

ADD REPLYlink written 4 months ago by Emily_Ensembl18k
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