The simple pipeline to examine the natural variation in the coding region of your favourite gene, that you either picked by GWAS or just working on for the entire life and would like to examine what else is there to it. The pipeline described in this protocol is based on the SNP data from Arabidopsis, and so you will miss the variation due to non-Col-0 specific insertions or deletions. Nevertheless, this pipeline will give you an insight in the possible alterations of the coding region of your favourite protein