How to use the GWAS SNP dataset in TASSEL?

The PLINK files available from the Downloads page are in “binary PLINK” format (bed, bim, fam).
To use with TASSEL, one needs a “text PLINK” format (ped, map).

Here is how to do it on Windows:

1. Download PLINK 1.90 from https://www.cog-genomics.org/plink2/ (choose for your OS).

2. Unpack the archive.

3. Create a folder on your desktop named plinkdata

4. Put plink.exe and the dataset into this folder. Example dataset files:

   • pruned_v2.1.bed

   • pruned_v2.1.bim

   • pruned_v2.1.fam

5. Open PowerShell and run:

cd Desktop
cd plinkdata
ls
.\plink --bfile pruned_v2.1 --recode tab --out 1Mdata