vcftools: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On CentOS possible default full paths are:

/usr/bin/vcftools - from package: vcftools

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/vcftools - from package: vcftools

You may install the required package with command apt-get install {package}

Error in other languages:
vcftools: bevel nie gevind nie
vcftools: comandă negăsită
vcftools: comando não encontrado
vcftools: commande introuvable
vcftools: command not found
vcftools: käsku ei ole
vcftools: không tìm thấy lệnh
vcftools: komanda nerasta
vcftools: Kommando nicht gefunden.
vcftools: kommandot finns inte
vcftools: komut yok
vcftools: nie znaleziono polecenia
vcftools: níor aimsíodh an t-ordú
vcftools: no se encontró la orden
vcftools: no s'ha trobat l'ordre
vcftools: opdracht niet gevonden
vcftools: parancs nem található
vcftools: perintah tidak ditemukan
vcftools: príkaz nenájdený
vcftools: příkaz nenalezen
vcftools: команда не найдена
vcftools: командата не е открита
vcftools: 命令找不到
vcftools: コマンドが見つかりません