Convert Illumina Final Report.txt file into PLINK input files (.fam, .lgen, .ped etc)

Question

[Alexandros.Frydas]

Hello everyone,

I want to do perform a series of GWAS using Sheep genomic data. I received an Illumina FinalReport.txt file created with GenomeStudio and for a while I have been looking for a tool/way/anything to be able to convert this file into the standard PLINK Input files.

In case anyone suggests the plug-in that can be purchased for free for GenomeStudio 2.0 to do this work, unfortunately I have no access to the GenomeStudio I got the files from, neither has anyone else (yeah..I know..)

I came across this thread: How to Convert Illumina Final Report File To Plink, but the repository suggested looks quite old and when I tried I get errors due to older versions of python (2.6).

Can anyone shed some light on this?

Thanks in advance!

Alex