release/104.2

Do not attempt to translate gene names from the SpliceAI plugin that look like numbers into numbers when using JSON output.

release/104.0

New in version 104 (May 2021)

• Human GRCh37 cache files now include dbSNP 154!
• --var_synonyms output structure has been altered when used with --json
  VEP Plugins:
• dbNSFP - now supports matching by peptides
• SpliceAI - now compares gene symbols to improve score accuracy
• DisGeNET - improvements have been made to output structure

release/103.1

Fix VEP test.

release/103.0

New:
Variant Recoder is now available as a web tool
Variant Recoder output is now allele specific

Web VEP Options:
Variant Synonyms are now available through the web interface
MasterMind results are available through the REST and web interfaces

VEP Options:
--mane : Now provides additional MANE Plus Clinical annotations alongside MANE Select
--mane_select : Returns MANE Select annotations

release/102.0

New in version 102 (November 2020)

VEP options:

• --uniprot: Now we report precise Ensembl translation to UniProt isoform mappings.
• --spdi - new: Add genomic SPDI notation.

Web VEP options:

• Shifting variants in the 3' direction with --shift_3prime and --shift_genomic is now supported through the web interface.
• DisGeNET - new: DisGeNET results are available through the web interface.
• SpliceAI - new: SpliceAI pre-calculated scores are available through the web interface.

VEP filter options:

• --soft_filter - new: Option to only flag the failing variation in the FILTER column and keep the entries in the output VCF file.

release/101.0

New in version 101 (August 2020)

New options:

--var_synonyms: Report known synonyms for colocated variants. Must be used with --cache.

VEP plugins:

neXtProt : neXtProt retrieves comprehensive human-centric protein-related data for missense variants

Fix rejoining intergenic variant alleles after minimal option

Fix rejoining intergenic variant alleles after converting alleles to their most minimal representation.

Rejoin alleles in VCF output after minimal option was applied

Rejoin alleles in VCF output after minimal option was applied

Merge pull request #771 from aparton/release/100.2

Cache file updates

Adds support for --shift_3prime with --json and --vcf

--vcf and --json should now work correctly with --shift_3prime