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