GWAS result with pval equal zero. How to handle and how to plot?

Question

[GabrielMontenegro]

Hi everyone,

I did a GWAS using plink --assoc function and got a hit (it is well known) with a pval = 0. When I take the -log10 to do the Manhattan plot I get and Infinite value.

How should I deal with this?

Thanks in advance

Answer 1

[chrchang523]

PLINK 1.9 has the --output-min-p flag to deal with this. Add something like --output-min-p 1e-99 to your --assoc command line, and any p-value below 10^{-99} will be reported as 10^{-99}.