vcf-phased-join: 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/vcf-phased-join - from package: vcftools

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

On Debian possible default full paths are:

/usr/bin/vcf-phased-join - from package: vcftools

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

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