I apologize for what might be a relatively easy question - I am new to plink and plink format.
I am trying somethings out using the CanMap dataset of canine SNPs from various breeds. I have the plink files (pheno, ped, and map files). I have converted the data to structure format to run structure but the number of loci far exceed what I can easily work with.
I know that the canine genome has huge ld blocks, so I was hoping to do some initial analyses with a small subset of the canmap data, say with 20 randomly selected loci from each chromosome.
Any thoughts on how i might get started to do the subsetting? I am happy to work on it if someone can point me in to a direction to dive in to, but I don't even know where to start. I can work up a script I think to select columns from the structure file, but I am trying to learn how to deal with plink so I thought I would start there.
Any thoughts are appreciated! Thanks Kevin
