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 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