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