Output the call rate of genotypes in plink

Question

[Floris Brenk]

Hi all,

I was wondering whether someone knows an easy solution to output the call rate per individual from a plink file. I know you can filter on the call rate using --mind, but I would like to have a list with the call rate per sample. I tried some coding myself by taking each sample by itself and do a plink command and grepping the call rate out of there, but it is super slow... It would be much easier if this could be done on the whole file instead of doing it per sample.

Answer 1

[chrchang523]

--missing reports both per-sample and per-variant missingness rates.