Could I ask two further questions.

I was trying to alter the command so that the --snps was a file with a list of SNPs in it rather than comment delimited on the command line, but I was unsuccessful. The SNPs have no particular range (because I provided a simple example of something I'm doing on a much more complicated scale), I'll have too many SNPs to type manually on the command line, and the SNPs won't be confined to a particular chromosome, range etc.

My second question is about the --keep command. So I have a list of say 1,000 individuals in total in my population, and I have genotypic information for all of these individuals.

I read that the indfile.txt should describe a list of the individuals that I want to keep. But I want to keep "all of whom have the SNPs as described in the --snps file". So I can't pre-define the indfile.txt with a list of individuals, because I don't know which ones have the SNPs.

So what I want is ultimately:

I read in a .bim/.bed file for the full list of participants and their genotypes.

I read in a list of SNPs separately.

The command will say:

For each SNP, go through the genotypic data of each individual.

Pull out something like this:

SNP1: Person 1,2,3,4,5 have this SNP. -> print out a file called SNP1. In this file, list 1,2,3,4,5.

SNP2:Person 1,3,5,6,7 has this SNP -> print out a file called SNP2. In this file, list 1,3,5,6,7.

etc. So it gives me, for each SNP, a list of individuals with the SNP.

If you had any ideas, I would appreciate it.