# Error filtering SNPs with Plink

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.

• Answered this on Biostars: the issue was that there were only 14 samples, and almost no genetic variation between them. May 4, 2018 at 15:35
• @ChristopherChang if you have the time, it would be great if you could post your answer here too!
– terdon
May 4, 2018 at 16:01
• @terdon here is the link: biostars.org/p/281334/#313252 May 4, 2018 at 16:23