Use VEP to analyse your variation data locally. No limits, powerful, fast and extendable, command line VEP is the way to get the most out of VEP and Ensembl.


VEP is a powerful and highly configurable tool - have a browse through the documentation. You might also like to read up on the data formats that VEP uses, and the different ways you can access genome data. The VEP script can annotate your variants with custom data, be extended with plugins, and use powerful filtering to find biologically interesting results.


  1. VEP 的安装需要 HTSLIB 的各种依赖,在 CentOS 6 的集群环境下目前没有安装成功。
  2. Perl-5.26.1 下使用 perl INSTALL.pl --NO_HTSLIB 可以正常安装。
  3. cpan 和 cpanm 安装 DBD::mysql 都会出现各种异常;下载 DBD-mysql-4.050.tar.gz 手动安装时,make test 可能会出现失败,是因为当前用户可能没有创建、删除 test 数据库的权限,因此可以忽略 make test 这一步,make 后直接执行 make isntall 安装即可。

cpanm-DBD-mysql.png

  1. Bio::DB:HTS 包的安装比较繁琐,问题也有点多。