Delete Chromosome With Plink

Question

[sonalier.nathan]

Hi everybody ! I am working with PLINK and I would like to supress chromosome X and Y and mitochondrial chromosome before doing the quality control.

Do you have an idea of the command I should put ?

Thanks for your help !

Answer 1

[mc]

With plink2 you should be able to add the flags --chr 1-22 to get chromosomes 1 through 22

[chrchang523]

"--not-chr X,Y,MT" also works.