Answers.Body: <p>Admixture requires a '12'-coded .ped file, rather than the allele-coding you're using. 'plink --file [file prefix] --recode 12' produced a .ped file that Admixture could use for me.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-02-28T23:39:20.580Z
Answers.LastActivityDate: 2024-02-28T23:39:20.580Z
Answers.UserDisplayName: Caitlyn Perry
Body: <p>I'm trying to run <a href="https://dalexander.github.io/admixture/index.html" rel="nofollow noreferrer">ADMIXTURE</a> on some files I've generated using the <a href="https://catchenlab.life.illinois.edu/stacks/" rel="nofollow noreferrer">Stacks</a> pipeline. ADMIXTURE accepts .bed and .ped files, but when I try to pass the .ped file generated by Stacks to ADMIXTURE (v1.3.0), I get a &quot;PLINK Input file error&quot;. I've pasted the head of my (tab separated) .ped file below.</p>
  <blockquote>
  <p>head populations.plink.ped -n 1</p>
  <p>garden  QUAC_G_SH_Q1485 0       0       0       0       0       0       T       T       C       C       G       G       T       T       C       C       C       C       G       G       T</p>
  </blockquote>
  <p>Alternatively, I could convert my .ped file to .bed using plink, and try to pass this to ADMIXTURE--but Stacks didn't provide me with a map file to do this, so I don't think that will work.</p>
  <p>If anyone knows what needs to change with my .ped file (remove sample name? population designation?), I'd appreciate any tips. This is my first time running most of these programs.</p>
  <p>Thanks!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-31T12:52:52.100Z
Comments.Text: Did you obtain a solution to this? I am currently facing the same issue. Thanks
Comments.UserDisplayName: Abosede Olarewaju
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-31T15:38:39.737Z
Comments.Text: @AbosedeOlarewaju this would be a good question to ask, and include some specifics of your project.
Comments.UserDisplayName: M__
Tags: <plink>
Title: Proper formatting of .ped files, in order to run ADMIXTURE
ThreadText: # Proper formatting of .ped files, in order to run ADMIXTURE
  
  (Asked by: username_0 on 2022-06-01)
  
  I'm trying to run [ADMIXTURE](https://dalexander.github.io/admixture/index.html) on some files I've generated using the [Stacks](https://catchenlab.life.illinois.edu/stacks/) pipeline. ADMIXTURE accepts .bed and .ped files, but when I try to pass the .ped file generated by Stacks to ADMIXTURE (v1.3.0), I get a "PLINK Input file error". I've pasted the head of my (tab separated) .ped file below.
  
  > head populations.plink.ped -n 1
  >
  > garden QUAC\_G\_SH\_Q1485 0 0 0 0 0 0 T T C C G G T T C C C C G G T
  
  Alternatively, I could convert my .ped file to .bed using plink, and try to pass this to ADMIXTURE--but Stacks didn't provide me with a map file to do this, so I don't think that will work.
  
  If anyone knows what needs to change with my .ped file (remove sample name? population designation?), I'd appreciate any tips. This is my first time running most of these programs.
  
  Thanks!
  
  **Tags:** plink
  
  > **Comments:**
  > **username_1**: Did you obtain a solution to this? I am currently facing the same issue. Thanks  
  > **username_2**: @username_1 this would be a good question to ask, and include some specifics of your project.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2024-02-28. Score: 2
  
  Admixture requires a '12'-coded .ped file, rather than the allele-coding you're using. 'plink --file [file prefix] --recode 12' produced a .ped file that Admixture could use for me.
  
  
  ---
  
  