Failed missingness test plink GWAS

Question

[Leonida Monaco]

Hi.

I have a part of a file containing 80 patients (80 cases), divided into 41 females and 39 males Individuals. I am doing all the --geno --mind --maf --hwe tests. But all of the 80 individuals and so the SNPs are removed with a mind < 0.1. Plus, with --geno = 0.1 all the SNPs are removed too. There is something that I can do understand this situation and how I can fix it, or it could be probable, that the files have something wrong ? Thanks

[Leonida Monaco]

Thanks man. I will try it .

Answer 1

[Kevin Blighe]

I would take a look at the missingness rate per individual by executing:

plink --file MyData --missing

Then, check the contents of plink.imiss. There is more information on this here.

Once you see the missingness rate per individual, you can decide an appropriate cut-off during your association tests by using -mind 0.15 or -mind 0.2, et cetera.