Why my GWAS p-value QQ-plot falls far above diagonal?

Asked Oct 06 '23 at 20:20

Active Oct 06 '23 at 20:20

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I'm trying to run GWAS pipeline using plink, but the results I got look really off. The QQ-plot of the p-values is far above the diagonal.

I'm pretty sure I followed the correct QC process, and the inclusion of covariates is probably also not a major cause since with and without covariates I got very similar QQ-plots which look wrong (attached below).

Does anyone have experience with this and know what's going wrong? Thanks!

asked Oct 06 '23 at 20:20

Celia L.

1

Is there more data than shown on the graph? Set the y-axis maximum to automatic... – Michael Lew Oct 06 '23 at 20:59
Wow! Are the training and test set different? We can see even with the truncated Y axis (not the cause) that this is unusual. – BigMistake Oct 07 '23 at 03:27
1

The p-values are not independent. This QQ plot looks as I would have expected. Have you made a Manhattan plot of the results? – dipetkov Oct 07 '23 at 09:52

Why my GWAS p-value QQ-plot falls far above diagonal?

0 Answers0