vcf-annotate: 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-annotate - from package: vcftools

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

On Debian possible default full paths are:

/usr/bin/vcf-annotate - from package: vcftools

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

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