Releases: Ensembl/ensembl-vep
release/113.0
New in version 113 (October 2024)
- gnomAD frequency data updated to v4.1 for both genomes and exomes.
- Support for GENCODE primary transcript set added. See, --gencode_primary and
--flag_gencode_primary. - Support added for --mane, --mane_select, and --canonical when GFF/GTF file used as annotation source.
- Nextflow VEP now suppots other input data formats besides VCF. For supported formats see - Data formats.
Plugin support added to REST and Web for:
Plugin support added to Web for:
Plugin support added to REST for:
-
Plugin data version updated for CADD (v1.6 to v1.7) and dbNSFP (4.5c to 4.7c).
release/112.0
New in version 112 (May 2024)
Enhanced Structural Variant Support:
- Added support for CNV:TR
- Enabled the use of chromosome synonyms in breakends
- Report consequences for each breakend and enable the input of single breakends
New plugins (supported on CLI, Web and REST):
- AlphaMissense - annotates missense variants with the pre-computed AlphaMissense pathogenicity scores. AlphaMissense is a deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants.
New plugins (supported on CLI and Web):
- RiboseqORFs - uses a standardized catalog of human Ribo-seq ORFs to re-calculate consequences for variants located in these translated regions
New plugins (supported on CLI):
- Paralogues - fetches variants overlapping the genomic coordinates of amino acids aligned between paralogue proteins
- AVADA - Automatic VAriant evidence DAtabase is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates
- GeneBe - A plugin kindly contributed by the GeneBe team, it retrieves automatic ACMG variant classification data from https://genebe.net/
- PhenotypeOrthologous - A VEP plugin that retrieves phenotype information associated with orthologous genes from model organisms
Plugin support added to REST and Web for:
- CADD_SV
- CADD scores for Sus scrofa
- Dosage Sensitivity
- Enformer
release/111.0
New option --individual_zyg returns a single list of individuals and their zygosity (instead of a separate line of output for each individual and variant combination like in --individual)
Custom annotation has been improved with the following options:
num_records to limit the number of matching records (50 by default)
summary_stats to calculate summary statistics (min, mean, max, count, sum) using annotation scores (not used by default)
New plugins (supported on CLI, REST and web):
Enformer - adds pre-calculated predictions of variant impact on gene expression
BayesDel - adds a deleteriousness meta-score combining multiple deleteriousness predictors
OpenTargets - adds locus-to-gene (L2G) scores to predict causal genes at GWAS loci from Open Targets Genetics
New plugins (supported on CLI):
DeNovo - identifies de novo variants in a VCF file. This plugin requires a pedigree (.ped) file.
SpliceVault - predicts exon-skipping events and activated cryptic splice sites based on the most common mis-splicing events around a splice site
DosageSensitivity - annotates the likelihood of a gene being haploinsufficient or triplosensitive
VARITY - adds pre-calculated pathogenicity scores of rare human missense variants
release/110.1
Bugfix:
- Misleading warning message about undefined variable. Reported in - #1457
release/110.0
New plugins (supported on CLI):
- TranscriptAnnotator - a VEP plugin that annotates variant-transcript pairs
New plugins (supported on CLI, REST and web):
- Geno2MP - adds information from Geno2MP, a web-accessible database of rare variant genotypes linked to phenotypic information
- MaveDB - adds information from MaveDB, a database that holds experimentally determined measures of variant effect
Structural variant (SV) annotation updates
- More detailed molecular consequence predictions
- More efficient integration of information from reference SV sets
- Support for breakend variant annotation
- Integration of CADD-SV scores
release/109.3
- Fixed test and installer issues stemming from ENV variables.
- Added checks for variable filtering coming from INI file and ENV variables.
release/109.2
- Fix auto assignment of
VEP_VERSION
toAPI_VERSION
in installer script - Remove usage of deprecated parameter
VERSION
in the installer script
release/109.1
Fix ensembl-vep docker build issues.
release/109.0
New plugin (supported on CLI):
- GWAS - reports genome-wide association study data from GWAS catalog
Plugins now available in REST and web:
- UTRAnnotator - annotates the effect of 5' UTR variant especially for variant creating/disrupting upstream ORFs
Plugins now available in REST:
- NMD - predicts if a variant allows transcript to escape nonsense-mediated mRNA decay based on certain rules
- Plugin LOEUF replaces Loftool in the web with more recent ‘loss-of-function’ score for variants
Deprecated Plugins:
- miRNA - this plugin was fully deprecated in favour of --mirna flag (in web and REST)
- ExAC - this plugin was deprecated given that VEP cache includes ExAC data as part of gnomAD
Other changes:
- VEP Docker image now includes all VEP plugins
- SIFT version has been updated from 5.2.2 to 6.2.1 (except for human GRCh37)
- PolyPhen-2 version has been updated from 2.2.2 to 2.2.3 (except for human GRCh37)
release/108.2
- Fix download of cache and FASTA files for fallback cases in
INSTALL.pl
script. - Allow user-provided links with
ftp://
protocol to download cache and FASTA files inINSTALL.pl
script.