release/96.3

Fix VEP process issue when the alleles from an input variant are the same (i.e. REF = ALT)

release/96.2

Haplosaurus - fix comparison for non numeric chromosomes

release/96.1

Haplosaurus - fix interpretation issue when following entries have similar coordinates but on different chromosomes in the input file

release/96.0

• Add SPDI format for VEP (input) and Variant Recoder (input and output)
• Update VEP cache with gnomAD 2.1 (human)
• Update the Docker VEP base image to Ubuntu 18.04
• Retire deprecated flags: --gmaf, --maf_1kg, --maf_esp, --maf_exac, --check_alleles, --html, --gvf
• Retire legacy code about the pileup input format, which is no longer supported
• Deprecate the installation flag "--VERSION"
• Force numbers to be encoded as numbers in JSON output

release/95.3

Fix to ignore the empty MotifFeatures from the VEP cache

release/95.2

Fix the installation script issue when an older version of VEP is specified with the flag '--VERSION'

release/95.1

Add the Perl library Text::CSV in the cpanfile (required for the G2P VEP plugin)

release/95.0

• 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

release/94.5

Fix issue to fetch some gene names from external sources

release/94.4

Minor fix: remove warning message about an uninitialised value in 'if' condition