VEP variant effect predictor 깔기

sudo apt install curl # Curl library 깔기
sudo apt-get install libdbi-perl # Perl의 dbi library 깔기

# yum install perl-DBI  # Redhat계열의 경우

curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/88.zip # Git에서 ensembl 다운로드 받기(89버전이 최신 버전임)

curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/92.zip --insecure 

unzip 88.zip

cd ensembl-vep-release-88/

sudo perl INSTALL.pl --NO_HTSLIB

cache깔기

 41 42 43 44 45 46 #homosapiens 계열임

원하는 버전 깔기는 아래 사이트 접속

http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#toolsversions

Fedora에서 깔기 (Ensembl 37.75)

1. 아래 사이트 접속 및 Ensembl 75 다운로드 zip파일임. 압축도 풀것

http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#toolsversions

2. Ensembl API깔기

http://www.ensembl.org/info/docs/api/api_installation.html

mkdir src

cd src

wget ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz

wget https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

tar zxvf ensembl-api.tar.gz
tar zxvf BioPerl-1.6.1.tar.gz

PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-1.6.1
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-funcgen/modules
export PERL5LIB

3. 필요한 module들 깔기

perl -MCPAN -e 'install Archive::Extract'

cpan -f Archive::Tar

cpan -f Archive::Zip

cpan -f Bio::PrimarySeqI module

4. 실행

perl INSTALL.pl

에러가 난다면 bioperl 수동 설치 필요

perl -MCPAN -e shell

install Module::Build

cpan

d /bioperl/

install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

영향 관련 doc

http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf

http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences