Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-04T15:35:47.763Z
Comments.Text: Answered this on Biostars: the issue was that there were only 14 samples, and almost no genetic variation between them.
Comments.UserDisplayName: Christopher Chang
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-04T16:01:13.097Z
Comments.Text: @ChristopherChang if you have the time, it would be great if you could post your answer  here too!
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-04T16:23:17.667Z
Comments.Text: @terdon here is the link: https://www.biostars.org/p/281334/#313252
Comments.UserDisplayName: Ana Chero
Tags: <vcf><snp><filtering><plink>
Title: Error filtering SNPs with Plink
ThreadText: # 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**: @username_1 if you have the time, it would be great if you could post your answer  here too!  
  > **username_0**: @username_2 here is the link: https://www.biostars.org/p/281334/#313252  
  
  ---
  
  ## 0 answers
  
  