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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), MINiML formatted family file(s) or Series Matrix File(s).

I'm looking for a way to convert these into PED and MAP files for use in PLINK...

Or does PLINK read these formats natively?

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  • $\begingroup$ I see. Maybe PLINK cannot handle this. I see on GEO that series downloads are suitable for opening in spreadsheet. $\endgroup$
    – Phoenix Mu
    May 25 at 1:16
  • $\begingroup$ I don't want to manually play with 3000 sheets... $\endgroup$
    – Dan Bolser
    May 27 at 13:48
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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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