release/100.0

New in version 100 (April 2020)

Human GRCh37 variant and phenotype data has been updated with multiple data sets including dbSNP153, ClinVar’s 201912 release and COSMIC release 90
The GRCh37 RefSeq transcript set has been updated to NCBI's 1st November 2019 release (initially annotated on GCF_000001405.25)!

New VEP options:

--shift_3prime: Right aligns all variants relative to their associated transcripts prior to consequence calculation
--shift_genomic: Right aligns all variants, including intergenic variants, before consequence calculation and updates the Location field

New VEP plugins:

SpliceAI: SpliceAI is a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence.
DisGeNET: DisGeNET is a database containing human variant-disease associations.

release/99.2

There is currently a problem translating insertions to toplevel. Only print a warning message if VEP tries to transform an insertion to toplevel sequence for example from scaffold to chromosome level.

release/99.1

Updates to:
Variant Recoder - Bugfix when providing HGVS input with a RefSeq transcript
Plugins - Removes warning when using Plugins with VCF output

release/99.0

New in version 99 (January 2020):

Human GRCh38 cache files now contain variants from dbSNP153
New options have been added to REST:
vcf_string: VEP can now provide a VCF-like string representing the input variant
transcript_version: Add version numbers to Ensembl transcript identifiers
SpliceRegion: Provides granular predictions of splicing effects (Details)
LoF: LOFTEE implements a set of filters to predict LoF (loss-of-function) variants. (Details)

release/98.3

Adds installer fix to support CACHE_URL flag for new indexed cache files

release/98.2

Updates to installer to support indexed cache files

release/98.1

update release version

release/98.0

New data

• Human GRCh38 cache files now contain variants from dbSNP152
• MANE attributes are now included within VEP cache files

New and updated VEP options

• --clin_sig_allele has been updated to be used by default
• --custom_multi_allelic prevents VEP from assuming that comma separated lists in custom annotations are allele specific

VEP installer

• HTSLib v1.9 is now installed by default (previously v1.3.2)
• Bio::DB::HTS v2.11 is now installed by default (previously v2.9)
• New option 'PLUGINSDIR' allows you to specify the installation directory for plugins

New VEP plugin

• satMutMPRA measures variant effects on gene RNA expression for 21 regulatory elements

release/97.4

Fix for when --sift s option is used, 0 SIFT values are not in VCF output.

release/97.3

Prevent the variant sorting check for several input formats