1.6.2

Description

• JASIX utility now available (like tabix - allows downstream tools to quickly extract variant annotation)
• Nirvana is now able to annotate from stdin and stdout
• Updated gene-specific annotation in the JSON schema (especially OMIM)
• Minor bug fixes with VCFs from the Illumina small pedigree workflow
• Added support for ExpansionHunter repeat expansion VCFs
• Improved gene fusion annotation functionality

Data sources

• Ensembl build 84 (originally from VEP)
• RefSeq build 84 (originally from VEP)
• ClinVar (2017-05-03)
• COSMIC (v80)
• dbSNP (v150)
• 1000 Genomes Project (Phase 3 v5a)
• EVS (ESP6500SI-V2-SSA137)
• ExAC (0.3.1)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2017-05-03)

1.5.4

Description

• Upgraded to .NET Core 1.1
• Intergenic and transgenic gene fusion support
• Added OMIM gene-to-phenotype annotations
• Added sample counts for COSMIC variants
• Silenced regulatory region annotation for variants > 50 kbp
• Added command-line option to output all transcripts for large SVs
• This release contains 11 unresolved bugs

Data sources

• Ensembl build 84 (originally from VEP)
• RefSeq build 84 (originally from VEP)
• ClinVar (2016-08-31)
• COSMIC (v78)
• dbSNP (v147)
• 1000 Genomes Project (Phase 3 v5a)
• EVS (ESP6500SI-V2-SSA137)
• ExAC (0.3.1)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)

v1.4.2

Description

• Initial release on .NET Core.
• All data sources updated - ClinVar updated to 2016-07-05
• Numerous performance updates
• Compressed reference sequence is now not PAR-masked
• 18 bugs were fixed since the previous release
• This release contains 15 unresolved bugs

Data sources

• Ensembl build 84 (originally from VEP)
• RefSeq build 84 (originally from VEP)
• ClinVar (2016-07-05)
• COSMIC (v77)
• dbSNP (v147)
• 1000 Genomes Project (Phase 3 v5a)
• EVS (ESP6500SI-V2-SSA137)
• ExAC (0.3.1)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)