VEP Installation Guide

#下载依赖包

sudo apt-get install-y Curl rsync tar make perl perl-base Tabix

#设置perl环境变量

Export PERL_PATH=~/PERL5

#在perl安装依赖包

Curl-l http://cpanmin.us | Perl---notest-l $PERL _path lwp::simple LWP::P rotocol::https archive::extract archive::tar archive::zip CGI DBI Time::Hi Res

Export perl5lib= $PERL _path/lib/perl5: $PERL _path/lib/perl5/x86_64-linux

#新建vep安装目录

Export VEP_PATH=~/VEP
Export VEP_DATA=~/.VEP

#下载vep

mkdir $VEP _path $VEP _data; CD $VEP _path

Curl-lo https://github.com/Ensembl/ensembl-tools/archive/release/84.tar.gz

TAR-ZXF 84.tar.gz--starting-file variant_effect_predictor--transform= ' s|. */|. /|g '

#设置环境变量

Export perl5lib= $VEP _path: $PERL 5LIB
Export path= $VEP _path/htslib: $PATH

#下载注释包

RSYNC-ZVH rsync://ftp.ensembl.org/ensembl/pub/release-84/variation/vep/homo_sapiens_vep_84_grch{37,38}.tar.gz $ Vep_data
RSYNC-ZVH rsync://ftp.ensembl.org/ensembl/pub/release-84/variation/vep/mus_musculus_vep_84_grcm38.tar.gz $VEP _ DATA
Cat $VEP _data/*_vep_84_grc{h37,h38,m38}.tar.gz | TAR-IZXF-C $VEP _data

#安装 Ensembl API, the reference Fastas

Perl convert_cache.pl--species homo_sapiens--version 84_grch37,84_grch38--dir $VEP _data--force_overwrite to Overwrite
Perl convert_cache.pl--species mus_musculus--version 84_grcm38--dir $VEP _data

#下载 ExAC r0.3 VCF, because it is a Google link, may not download, need to download on other pages

Curl-l Https://googledrive.com/host/0B6o74flPT8FAYnBJTk9aTF9WVnM > $VEP _data/exac.r0.3.sites.minus_ Somatic.vcf.gz
Tabix-p VCF $VEP _data/exac.r0.3.sites.minus_somatic.vcf.gz

#安装完成, testing

Perl variant_effect_predictor.pl--species homo_sapiens--assembly GRCh37--offline--no_progress--everything--shift_ HGVs 1--check_existing--check_alleles--total_length--allele_number--no_escape--xref_refseq--dir $VEP _data--fasta $VEP _data/homo_sapiens/84_grch37/homo_sapiens. grch37.75.dna.primary_assembly.fa.gz--plugin ExAC, $VEP _data/exac.r0.3.sites.minus_somatic.vcf.gz--input_file EXAMPLE_GRCH37.VCF--output_file Example_GRCh37.vep.txt

#可以看到下列文件, the comment is successful.

-Read Existing Cache info
-Loaded Plugin:exac
-Starting ...
-Detected format of input file as VCF
-Read 173 variants into buffer
-Checking for existing variations
-Reading transcript data from cache and/or database
-Retrieved 3097 transcripts (0 mem, 3162 cached, 0 DB, duplicates)
-Reading regulatory data from cache and/or database
-Retrieved 14876 regulatory features (0 mem, 14877 cached, 0 DB, 1 duplicates)
-Analyzing chromosome 21
-Analyzing variants
-Analyzing Regulatoryfeatures
-Analyzing Motiffeatures
-Calculating consequences
-Analyzing chromosome 22
-Analyzing variants
-Analyzing Regulatoryfeatures
-Analyzing Motiffeatures
-Calculating consequences
-Processed 173 total variants (VARS/SEC, vars/sec total)
-wrote stats summary to example_GRCh37.vep.txt_summary.html
-finished!

VEP Installation Guide