changed script/variant_effect_predictor.pl file to symlink to same file inside variant_effect_predictor dir for ease of updating vep version - now just download, extract & run new v_e_p.tar.gz
major upgrade - app uses vep api_version to look for available cache types (ensembl, refseq, merged) and disables any from selection if not available; results page displays api version and selected cache database; vep wrapper captures vep.pl stderr for display on results page; added vcf 'filter' col to results page; enabled HGVS notation function
added functions to retrieve and display vep api_version and app version
11 years ago
README.txt
to update vep:
1) delete/rename variant_effect_predictor dir (leave symlink intact)
2) download latest version from: http://www.ensembl.org/info/docs/tools/vep/index.html
3) run INSTALL.pl - skip cache (done manually below)
4) rename local Bio to eg Bio.v7x, move to ~/perl-lib and update Bio symlink in ~/perl5/lib/perl5
5) download & extract matching databases into ~/.vep/core & ~/.vep/refseq using
ftp://ftp.ensembl.org/pub/release-<xx>/variation/VEP/
*) main difference after upgrade is Bio::EnsEMBL classes - other Bio:: classes same
FASTA file for HGVS notations:
wget ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
gzip -d Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
perl variant_effect_predictor.pl -i input.vcf --offline --dir /home/raj/.vep/core
--hgvs --fasta Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
