一、簡(jiǎn)介
Variant Effect Predictor
The VEP is a software suite that performs annotation and analysis of most types of genomic variation in coding and noncoding regions of the genome. From disease investigation to population studies, it is a critical tool to annotate variants and prioritize a subset for further analysis.
使用說(shuō)明概覽：https://asia.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
詳情：http://asia.ensembl.org/info/docs/tools/vep/script/vep_download.html
二这难、下載安裝
1仔燕、下載
git clone https://github.com/Ensembl/ensembl-vep.git
2造垛、安裝
cd ensembl-vep
perl INSTALL.pl?
選數(shù)據(jù)庫(kù)，選插件晰搀，會(huì)進(jìn)行下載和解壓五辽。0是不選，all是選所有外恕，某個(gè)數(shù)字就下載某個(gè)版本的杆逗。
如果沒(méi)有對(duì)應(yīng)的cache文件也沒(méi)關(guān)系乡翅，可以用腳本從gtf和fa文件轉(zhuǎn)化。The VEP package also includes a script, gtf2vep.pl, to build custom cache files. This requires a local GFF or general transfer format (GTF) file that describes transcript structures and a FASTA file of the genomic sequence.
3罪郊、測(cè)試
如果未下載vcf文件對(duì)應(yīng)版本的數(shù)據(jù)庫(kù)需要加上參數(shù)--port 3337蠕蚜。
/home/shaoyu/software/ensembl-vep/vep -i /home/shaoyu/software/ensembl-vep/examples/homo_sapiens_GRCh37.vcf --cache --port 3337
結(jié)果文件：variant_effect_output.txt variant_effect_output.txt_summary.html
三、使用
/home/shaoyu/software/ensembl-vep/vep -i /home/shaoyu/software/ensembl-vep/examples/homo_sapiens_GRCh37.vcf --cache --port 3337 #bascic
/home/shaoyu/software/ensembl-vep/vep -i /home/shaoyu/software/ensembl-vep/examples/homo_sapiens_GRCh37.vcf --cache --port 3337 --sift b -o test2.sift.txt #SIFT is an algorithm for predicting whether a given change in a protein sequence will be deleterious to the function of that protein. the b means we want both the prediction and the score.
/home/shaoyu/software/ensembl-vep/filter_vep -i test2.sift.txt -filter "SIFT is deleterious" -o test2.sift.filter.txt #只留下deleterious的
/home/shaoyu/software/ensembl-vep/vep -i /home/shaoyu/software/ensembl-vep/examples/homo_sapiens_GRCh37.vcf --cache --port 3337 --everything -o test3.everything.txt? #--everthing加上所有注釋
--everthing?
Shortcut flag to switch on all of the following:
--sift b, --polyphen b, --ccds, --uniprot, --hgvs, --symbol, --numbers, --domains, --regulatory, --canonical, --protein, --biotype, --uniprot, --tsl, --appris, --gene_phenotype --af, --af_1kg, --af_esp, --af_gnomad, --max_af, --pubmed, --variant_class
更多參數(shù)：
https://asia.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_species
過(guò)濾參數(shù)：
四悔橄、解讀
1. transcript annotation
2. Protein annotation
五靶累、輸出文件
可以通過(guò)參數(shù)設(shè)定文件格式（txt, vcf, json），默認(rèn)為txt癣疟。
