Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (python executable.py --input allindividuals.vcf
)
plink --ped allindividuals.ped --map allindividuals.map --allow-extra-chr --indep-pairwise 50 10 0.1
but at the time I count the SNPs in the file plink.prune.in it has only 15 SNPs and in the file plink.prune.out it remains millions of them. In addition, when I change the parameters, the result is the same, no matter how many times I change it.