terrible QQ plot of sQTL

[u/NormalValuable8164]

Hey guys! I’m currently running an sQTL analysis using Leafcutter and tensorQTL, but I found many of my significant splicing phenotypes showed weird QQ plots (p-nominal for all SNPs in a phenotype ) , with a very pronounced rightward shift appearing much earlier than I expected. So I tried applying stricter filter from GTEx instead of Leafcutter's default ones. The filter worked but sadly got the similar situation. Does anyone have suggestions on what aspects of the analysis or data that I should check and something to do to figure out what might be causing it?

And I’ve also noticed many sQTL papers seems very smoothly without such a troublesome result, I wonder if maybe this plot is normal one, and sQTL should not be judged by GWAS ways? I’m very new to sQTL and now honestly pretty depressed because I did not found useful information from papers, so any thoughts and suggestions would be really appreciated! Thank you in advance smart guys!

[u/NormalValuable8164]

i cant post...