release/97.2

Fixes an issue when forcing sorting of rsID input files

release/97.1

• Fix issue when checking that the VCF variants are sorted by position

release/97.0

New VEP features

• Allele-specific clinical significance available. See new option --clin_sig_allele.
• Include the new --mane option into the --everything group option.
• Update --pick and --pick_order to support MANE Select transcripts.
• Check if the input variants are ordered: non ordered variants slow down VEP and require more memory.
• Skip annotation of complex and long structural variants and display a warning message.

New VEP options

• --clin_sig_allele: report allele specific clinical significance (it is variant-specific by default).
• --mane: report if a transcript is the MANE Select.
• --max_sv_size: extend the maximum Structural Variant size VEP can process.
• --no_check_variants_order: permit the use of unsorted input files (WARNING - this is slow and requires more memory).
• --overlaps: report the proportion and length of a transcript overlapped by a structural variant in VCF format.

→ VEP options documentation

VEP web tool

• The transcript identifiers are now returned with versions unless otherwise specified, e.g.:
  'ENST00000403559.8' instead of 'ENST00000403559'.

VEP installer

• tabix-indexed variant cache files are now installed by default.

Variant recoder

• Add an option --vcf_string to return results in VCF format.

VEP plugins

• FunMotifs - new: provide information about overlapping tissue-specific transcription factor motifs.
• Mastermind - new: reports variants that have clinical evidence cited in the medical literature.
• StructuralVariantOverlap - new: provide information from overlapping structural variants.
• G2P - update: now the plugin can be run offline.

→ VEP_plugins repository

release/96.3

Fix VEP process issue when the alleles from an input variant are the same (i.e. REF = ALT)

release/96.2

Haplosaurus - fix comparison for non numeric chromosomes

release/96.1

Haplosaurus - fix interpretation issue when following entries have similar coordinates but on different chromosomes in the input file

release/96.0

• Add SPDI format for VEP (input) and Variant Recoder (input and output)
• Update VEP cache with gnomAD 2.1 (human)
• Update the Docker VEP base image to Ubuntu 18.04
• Retire deprecated flags: --gmaf, --maf_1kg, --maf_esp, --maf_exac, --check_alleles, --html, --gvf
• Retire legacy code about the pileup input format, which is no longer supported
• Deprecate the installation flag "--VERSION"
• Force numbers to be encoded as numbers in JSON output

release/95.3

Fix to ignore the empty MotifFeatures from the VEP cache

release/95.2

Fix the installation script issue when an older version of VEP is specified with the flag '--VERSION'

release/95.1

Add the Perl library Text::CSV in the cpanfile (required for the G2P VEP plugin)