<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>

CC BY-SA 4.0
2021-06-11T18:25:58.100Z
2021-06-11T18:25:58.100Z
Dan Bolser
<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>

CC BY-SA 4.0
2021-05-25T01:16:40.257Z
I see. Maybe PLINK cannot handle this. I see on GEO that series downloads are suitable for opening in spreadsheet.
Phoenix Mu
CC BY-SA 4.0
2021-05-27T13:48:00.310Z
I don't want to manually play with 3000 sheets...
Dan Bolser
<plink><format-conversion><geo><snp-chip>
Convert SNP data from GEO into PED and MAP files?
# 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...  

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## 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


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