How can I calculate p-value for each SNPs in human genome for GWAS?

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Laith Ali

By online p value evaluation of SNPs

Que Thanh Thanh Nguyen

Laith Ali Could you recommend me an online site for that. Since I have got about 10,000 SNPs, I am not sure how to do it online.

Thanks a lot

Harmeet Singh

hope this article could prove to be helpful for determining the threshold values for your GWAS

Article Estimation of a significance threshold for genome-wide assoc...

Karansher S. Sandhu

I would recommend using GAPIT source codes, which provides you p values, manhattan plots and all such kinds of figures for GWAS results.

https://zzlab.net/ (here is the link, where you can explore all those codes in R)

Thanks a lot all of you.

I really appreciate.

Nikita Berawala

I am facing the same difficulty, would be great if you could help me out :)