release/113.3

Bug fix:

• Fix method codon() in TranscriptVariationAllele: ensembl-variation/1131
• Fix transcript mismatch warning message: ensembl-vep/1788

release/113.2

Bugfix:

• CADD plugin - same score for all alt alleles: VEP_plugins/749
• HGVSc for RefSeq transcripts - represent the alleles relative to the feature: ensembl-variation/1128

release/113.1

Bugfix:

• Fix hgvsg for insertion with ref allele -: ensembl-variation/1124

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:

• RiboseqORFs
• REVEL
• ClinPred

Plugin support added to Web for:

• Paralogues

Plugin support added to REST for:

• LOEUF

• 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 to API_VERSION in installer script
• Remove usage of deprecated parameter VERSION in the installer script