Converting illumina raw genotype data into PLINK PED format

Question

[mohamadi_yahya]

Hello

How can I convert Illumina raw genotype data into PLINK format?

[dfornika]

Can you provide more detail on the genotype format that you'd like to convert from? Is it a VCF file?

Answer 1

[Katalobo]

Probably you sorted this out a long time ago, so I'm posting this for future users having the same problem. I have recently posted a small set of python programs (including a GUI for windows and mac users - 64bit only) that deal with this can of problems.

You can find it in GitHub, under "nicolazzie" user, repository "SNPChimpRepo". I'll try to post a link here but I'm not sure I'm allowed: https://github.com/nicolazzie/SNPChimpRepo

This tool (SNPConvert or one of the 3 source codes if you're using Linux or just like command line better) is able to convert both ROW and MATRIX Illumina files into PED/MAP. However, please note also that GenomeStudio has a plugin to do that automatically (e.g. export PED/MAP files directly).

Hope this helps.

Cheers, Ezequiel