Answers.Body: <p>Sadly the 'contact us' email at GEO didn't help at all.</p>
  <p>I ended up probably re-inventing the wheel with this script:
  <a href="https://gist.github.com/CholoTook/60968e3ab6d90cb8fd19be55a25592f1" rel="nofollow noreferrer">https://gist.github.com/CholoTook/60968e3ab6d90cb8fd19be55a25592f1</a></p>
  <p>YMMV</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-11T18:25:58.100Z
Answers.LastActivityDate: 2021-06-11T18:25:58.100Z
Answers.UserDisplayName: Dan Bolser
Body: <p>I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here:
  <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147</a></p>
  <p>GEO provides data as <a href="https://www.ncbi.nlm.nih.gov/geo/info/soft.html#format" rel="nofollow noreferrer">SOFT formatted family file(s)</a>, <a href="https://www.ncbi.nlm.nih.gov/geo/info/MINiML.html" rel="nofollow noreferrer">MINiML formatted family file(s)</a> or Series Matrix File(s).</p>
  <p>I'm looking for a way to convert these into PED and MAP files for use in <a href="https://doi.org/10.1186/s13742-015-0047-8" rel="nofollow noreferrer">PLINK</a>...</p>
  <p>Or does PLINK read these formats natively?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-25T01:16:40.257Z
Comments.Text: I see. Maybe PLINK cannot handle this. I see on GEO that series downloads are suitable for opening in spreadsheet.
Comments.UserDisplayName: Phoenix Mu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-27T13:48:00.310Z
Comments.Text: I don't want to manually play with 3000 sheets...
Comments.UserDisplayName: Dan Bolser
Tags: <plink><format-conversion><geo><snp-chip>
Title: Convert SNP data from GEO into PED and MAP files?
ThreadText: # Convert SNP data from GEO into PED and MAP files?
  
  (Asked by: username_0 on 2021-05-21)
  
  I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here:
  <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147>
  
  GEO provides data as [SOFT formatted family file(s)](https://www.ncbi.nlm.nih.gov/geo/info/soft.html#format), [MINiML formatted family file(s)](https://www.ncbi.nlm.nih.gov/geo/info/MINiML.html) or Series Matrix File(s).
  
  I'm looking for a way to convert these into PED and MAP files for use in [PLINK](https://doi.org/10.1186/s13742-015-0047-8)...
  
  Or does PLINK read these formats natively?
  
  **Tags:** plink, format-conversion, geo, snp-chip
  
  > **Comments:**
  > **username_1**: I see. Maybe PLINK cannot handle this. I see on GEO that series downloads are suitable for opening in spreadsheet.  
  > **username_0**: I don't want to manually play with 3000 sheets...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2021-06-11. Score: 2
  
  Sadly the 'contact us' email at GEO didn't help at all.
  
  I ended up probably re-inventing the wheel with this script:
  <https://gist.github.com/CholoTook/60968e3ab6d90cb8fd19be55a25592f1>
  
  YMMV
  
  
  ---
  
  