Hi, I've been using FastQTL to map cis-QTL for molecular phenotypes. Correct me if I'm wrong, but I just noticed that nominal pass is not outputting phenotypes without any variants in cis-window, while permutation pass is indeed outputting these phenotypes, with 0 in the number_of_variants column and NA in the following ones.
I'm wondering what is the rationale of doing so?
Also, is it correct to first remove the phenotypes with NAs, and then correct for multiple testing, since these phenotypes were not tested I'd assume?
Thanks in advance.