As i already mentioned i need to do GWAS, to associate my phenotypic observation with that of Variants called from my bacterial isolates, where as i am not sure vcflib accepts phenotype or not, when it comes to other software like Tassel and Gapit according my limited knowledge they won't accept single chromosome or in other words it needs SNPs on multiple chromosome/scaffolds/contigs. if anyone here come across with the same issues or cracked with any script please suggest. Hope am very much clear now, Thanks in Advance.