reproducing GTEx eQTL negative set variant selection

[MiqG]

Hi,

thanks very much for developing this repo!

I was wondering how were the negative set of variants selected for eQTLs exactly.

I downloaded the finemapping table ("GTEx_49tissues_release1.tsv.bgz") from the Finucane lab (https://www.finucanelab.org/data), and I was able to reproduce the set of positive variants, setting a PIP threshold of 0.9.

However, although all your negative variants are in the table, I cannot prioritize them:

1. I consider only variants with PIP < 0.01
2. I compute TSS distances to target genes of positive variants
3. For each positive variant, I select the negative variant with the most similar TSS distance to the same target gene

Thanks very much in advance for your help! Best,

Miquel