GWAS-SSF for QTL datasets

[marcora]

How does GWAS-SSF handle eQTL or other QTL datasets (which are multi-trait GWAS)? One sumstats and one metadata file for each gene/molecular feature?

[marcora]

GWAS-VCF supports multi-trait GWAS datasets like QTL datasets.

[ljwh2]

That’s correct, each GWAS is stored as a separate file. Combining traits in a single file makes absolute sense within a project. However, considering a large scale resource such as the GWAS Catalog, in our implementation it does not make sense to present files in this way, as our users typically want the flexibility to download files across projects (e.g. all summary statistics for LDL cholesterol - not all lipoproteins from a single project). Particularly given that QTL datasets now run into 1000s of traits, which makes a very large payload to transfer.
The main goal of GWAS-SSF was to identify key mandatory and non-mandatory data and metadata fields for usability. We encourage researchers using GWAS-VCF to store multi-trait GWAS to include the mandatory fields defined by GWAS-SSF.