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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.

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  • $\begingroup$ Answered this on Biostars: the issue was that there were only 14 samples, and almost no genetic variation between them. $\endgroup$ May 4 '18 at 15:35
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    $\begingroup$ @ChristopherChang if you have the time, it would be great if you could post your answer here too! $\endgroup$
    – terdon
    May 4 '18 at 16:01
  • $\begingroup$ @terdon here is the link: biostars.org/p/281334/#313252 $\endgroup$
    – Ana Chero
    May 4 '18 at 16:23

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