Gene level threshold

[Vibha-Acharya]

Dear eQTLCatalogue team,

We are using eQTL catalogue to discover eQTLs in our selected variants. I have several confusions regarding the datasets and was wondering if you could provide some insights into it.

What is the difference between the *.cc.tsv files versus the *.all.tsv.gz files in the repository,

Also, we were thinking to apply gene-based threshold similar to GTEx pipeline , where the genome-wide threshold is determined using FDR and beta parameters of the minimum P value from permutation is used to determine the nominal P value threshold for each gene.

Although the p_beta, p_perm are available in *.permutation files, the beta parameters (shape_1, shape_2 aka alpha, beta) are not available.

I wonder if there is a way we can determine the pvalue threshold for each gene for all variants,

Thank you so much,

Regards,
Vibha

[VitorAguiar]

I'm not related to the eQTL Catalogue, but regarding your first question, once @kauralasoo told me that the "*.all.tsv.gz" files contain full summary statistics, and "*.cc.tsv.gz" contain all genes that had FDR < 0.01 and at least one fine mapped credible set.