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)