How does plink compute n_geno ("number of potentially valid call(s)")?
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Entering edit mode
2.3 years ago
kynnjo ▴ 40

I want to compute a call rate from the output I get by running plink with the --missing flag. The plink-generated output does not provide a call rate as such, but I am hoping to be able to derive such a call rate from the information it does put out.

For the purpose of calculating call rates, the relevant plink output file is the one with extension .imiss. This file has the format illustrated below by the top few lines of one of them:

     FID           IID MISS_PHENO  N_MISS  N_GENO   F_MISS
A-3771  S-5496822091          Y    4266 1293857 0.003297
A-9097  S-2624225976          Y    3776 1293857 0.002918
A-6498  S-9116645660          Y    1934 1293857 0.001495
A-3949  S-8580037889          Y    2972 1293857 0.002297
A-5613  S-7293217686          Y    4449 1293857 0.003439


The documentation states that the value in the N_GENO column is the "number of potentially valid call(s)", but it says nothing about how plink arrives at this number. The one shown above does not match any of the obvious counts and corrections I have tried.

Does anyone know how plink does it?

1
Entering edit mode
2.3 years ago

This should just be the total number of variants, minus chrY for females.