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 in INSTALL.pl script.

release/108.1

Fix download of cache data and FASTA files in INSTALL.pl script.

release/108.0

New plugin (supported on CLI, REST, and web):

• mutfunc - predicts destabilization of protein structure, interaction and others features by a variant (GRCh38 only)

Plugin feature extension:

• IntAct - four new species are now supported: rat, chicken (red jungle fowl), yeast, and Arabidopsis

Release/107.0

New plugin (supported on CLI, REST, and web):

• EVE - annotates human variants using EVA classification method based solely on evolutionary sequences (GRCh38 only)
• Plugins now available in REST and web (already available in CLI):
• GO - retrieves Gene Ontology terms associated with transcripts/translations
• IntAct - annotates human variants which fall in interaction sites, as described in the IntAct database

Plugins now available in web (already available in CLI):

• NMD - predicts if a stop_gained variant allows transcript to escape nonsense-mediated mRNA decay based on certain rules

Other changes:

• Readthrough transcripts are now removed from cache
• Transcripts of biotype ‘artifact’ which are artifactual duplication are now removed from cache and not accessible using database
• gnomaAD allele frequencies are now available for exomes and genomes separately through —af_gnomade and —af_gnomadg options respectively. The —af_gnomad option have same function as --af_gnomade.

release/106.1

Fix the VEP version number and fix tests to include the correct database version.

release/106.0

New plugins for command line use:

• IntAct: annotates human variants which fall in interaction sites, as described in the IntAct database
• CAPICE: integrates scored from a machine-learning-based method for prioritizing pathogenic variants (GRCh37 only)

Nextflow pipeline:

• A new configurable pipeline is available to run Ensembl VEP efficiently on large scale VCF

release/105.0

New

• 3 new Sequence Ontology terms are reported for more detailed splice consequence annotation:
  - splice_donor_5th_base_variant (SO:0001787)
  - splice_donor_region_variant (SO:0002170)
  - splice_polypyrimidine_tract_variant (SO:0002169)

New plugins

• ClinPred: adds pre-calculated scores from ClinPred which helps identify disease-relevant missense variants
• NMD: predicts whether a stop-gained variant will allow a transcript to escape nonsense-mediated decay
• PrimateAI: adds pre-calculated clinical impact scores of variants

Web VEP options

• Condel scores are no longer available via the VEP web interface as they have not been updated since 2014 and newer scores like CADD and REVEL are available

release/104.3

Fix code to use the correct codon table for mitochondrial variants when running VEP from GFF files.