Unable to retrieve summary stats for colocalization from new catalogue release.

[VitorAguiar]

Hello,

thank you for you effort to create eQTL Catalogue!

My question is about the latest update of the catalogue, when fine-mapping based filtering was adopted.

I have not being able to reproduce some colocalization results for exon/transcript/txrevise that I got with the previous version of the catalogue, and that is because the summary stats for the particular gene and dataset don't seem to be available anymore. I'm using the api v2 following your tutorial, and I also manually downloaded the cc.tsv.gz files from the FTP to confirm.

I wanted to understand if the data were removed by the new fine-mapping-based filtering, and if there is anyway to obtain data from the previous catalogue release.

For example, I can't find gene IKZF1 (ENSG00000185811) in GENCORD LCL exon data (QTD000096). I previously saw a PP4 = 0.9 with a lupus GWAS.

In case the data were removed by the filtering, which case is more likely: exon QTL data were removed because there was a (1) stronger PIP for gene expression QTL for the same gene (IKZF1), or (2) stronger PIP for exon QTL for other gene (in this region, there is only exon data for FIGNL1 now).

If the data removal is confirmed, I would be curious about your thoughts on the validity of my previous colocalization findings. Consider the case of IKZF1 above. I only found coloc with the IKZF1 exon data, not for exon data of any other gene in the region, not for IKZF1 gene expression QTL data.

Thank you so much,
Vitor