• The VEP parser is now more permissive for the GFF files (ID attribute only required for genes and transcripts)
• Add new option --show_ref_allele to include the allele reference in the VEP default output and the tab output formats
• Add a warning message when the VEP annotations INFO field hasn't been found/recognised in the VCF input file
• VEP Docker image:
  • Reduce the size of the VEP Docker image by about 45%.
  • Include the Linkage disequilibrium script in the VEP Docker image, making possible to run the LD plugin