<p>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 (<code>python executable.py --input allindividuals.vcf</code>)</p>

<pre><code>plink --ped allindividuals.ped --map allindividuals.map --allow-extra-chr --indep-pairwise 50 10 0.1
</code></pre>

<p>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.</p>

CC BY-SA 4.0
2018-05-04T15:35:47.763Z
Answered this on Biostars: the issue was that there were only 14 samples, and almost no genetic variation between them.
Christopher Chang
CC BY-SA 4.0
2018-05-04T16:01:13.097Z
@ChristopherChang if you have the time, it would be great if you could post your answer  here too!
terdon
CC BY-SA 4.0
2018-05-04T16:23:17.667Z
@terdon here is the link: https://www.biostars.org/p/281334/#313252
Ana Chero
<vcf><snp><filtering><plink>
Error filtering SNPs with Plink
# Error filtering SNPs with Plink

(Asked by: username_0 on 2018-05-04)

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.

**Tags:** vcf, snp, filtering, plink
> **Comments:**
> **username_1**: Answered this on Biostars: the issue was that there were only 14 samples, and almost no genetic variation between them.  
> **username_2**: @ChristopherChang if you have the time, it would be great if you could post your answer  here too!  
> **username_0**: @terdon here is the link: https://www.biostars.org/p/281334/#313252  

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## 0 answers

