Hello! I am trying to use plink to select only hm3 snps from the ukb bgen files that I have, but I am at a total loss as to how to proceed. I am really new to all of this, I'm a first year psychology phd student and have just gotten into bash scripting/terminal coding/HPC. I checked out the plink website here: https://zzz.bwh.harvard.edu/plink/dataman.shtml#extract and I tried to use: plink --file data --extract mysnps.txt

with --file referencing a file of hm3 snps, and --extract referencing a bgen file for chr22

I don't think I was doing this correctly, but regardless I got an error that said --file has been retired.

I would really appreciate some help, or even being pointed in the right direction to where I can figure it out myself, at this point in my training I just don't even know what resources are available for looking for answers. Thank you :)