3.2.3

• Updated the gene models for a number of transcripts on GRCh37 used by the TSO500 pipeline
• Updated HGVS conventions (removed reference bases from HGVS c. deletions, duplications, and delins)
• Updated how Nirvana handles RNA-edits (the operations that transform a cDNA sequence spliced from the reference genome into the RefSeq transcript sequence).

This release reduces the transcript-variant HGVS error rate for TSO500 genes to 0.0027%

3.11.1

Description

• Added support for fisherStrandBias (FS), mappingQuality (MQ), and binCount (BC)

3.5.0

Description

• Updated ClinVar, unified gnomAD genomes and exomes, OMIM API support

Data sources

• Ensembl build 91 (originally from VEP)
• RefSeq build 91 (originally from VEP)
• ClinVar (2019-08-08)
• COSMIC (v84)
• dbSNP (v151)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec (0.3.1)
• gnomAD (2.1)
• MITOMAP (2019-02-25)
• phyloP (2009-11-10)
• ClinGen (2016-04-14)
• OMIM (2019-02-25)

3.2.2

Description

• PATCH: Amino acid trimming, HGVS g. notation, affected positions (cDNA, CDS, and protein)

Data sources

• Ensembl build 91 (originally from VEP)
• RefSeq build 91 (originally from VEP)
• ClinVar (2019-02-04)
• COSMIC (v84)
• dbSNP (v151)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec (0.3.1)
• gnomAD (2.1)
• MITOMAP (2019-02-25)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2019-02-25)

2.0.9

Description

• Fixed JASIX on-the-fly indexing, phyloP VCF output, and stdin/stdout support

Data sources

• Ensembl build 91 (originally from VEP)
• RefSeq build 91 (originally from VEP)
• ClinVar (2018-01-29)
• COSMIC (v84)
• dbSNP (v150)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec (0.3.1)
• gnomAD (2.0.2)
• MITOMAP (2018-02-28)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2018-02-13)

2.0.8

Description

• Fixed a bug related to variant recomposition when the variant caller dynamically changes the number of sample specific fields
• Fixed the stdin/stdout support

Data sources

• Ensembl build 91 (originally from VEP)
• RefSeq build 91 (originally from VEP)
• ClinVar (2018-01-29)
• COSMIC (v84)
• dbSNP (v150)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec (0.3.1)
• gnomAD (2.0.2)
• MITOMAP (2018-02-28)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2018-02-13)

2.0.7

Description

• Fixed a bug related to sample variant frequencies at reference minor allele sites
• Fixed a bug related to gene fusion endpoints landing in a transcript region gap in RefSeq transcripts

Data sources

• Ensembl build 91 (originally from VEP)
• RefSeq build 91 (originally from VEP)
• ClinVar (2018-01-29)
• COSMIC (v84)
• dbSNP (v150)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec (0.3.1)
• gnomAD (2.0.2)
• MITOMAP (2018-02-28)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2018-02-13)

2.0.4

Description

• PHANTOM support (phased variant recomposer)
• VEP91 genes and transcripts update
• Completed initial plugin support
  • Expansion Hunter plugin
  • LOFTEE plugin
• Added support for TOPMed
• Added support for gapped RefSeq transcripts
• Updated data sources:
  • COSMIC
  • ClinVar
  • MITOMAP
  • OMIM
• Now supporting the new CANVAS alternate allele representation

Data sources

• Ensembl build 91 (originally from VEP)
• RefSeq build 91 (originally from VEP)
• ClinVar (2018-01-29)
• COSMIC (v84)
• dbSNP (v150)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec (0.3.1)
• gnomAD (2.0.2)
• MITOMAP (2018-02-28)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2018-02-13)

2.0.3

Description

• Added gnomAD & MITOMAP
• Introduced ExAC pLI, pREC, and pNull scores
• Updated data sources (ClinVar)

Data sources

• Ensembl build 84 (originally from VEP)
• RefSeq build 84 (originally from VEP)
• ClinVar (2017-11-02)
• COSMIC (v82)
• dbSNP (v150)
• 1000 Genomes Project (Phase 3 v5a)
• ExAC pLI, pNull, pRec(0.3.1)
• gnomAD (2.0.2)
• MITOMAP (2017-11-01)
• phyloP (2009-11-10)
• DGV (2016-05-15)
• ClinGen (2016-04-14)
• OMIM (2017-09-05)

2.0.1

Description

• Total re-design of Nirvana
• Added HGVS g. notation for MT variants
• Major speed and memory optimization
• On-the-fly JASIX index creation
• Updated data sources (COSMIC, ClinVar, OMIM)

Data sources

• Ensembl build 84 (originally from VEP)
• RefSeq build 84 (originally from VEP)
• ClinVar (2017-09-07)
• COSMIC (v82)
• 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 (2017-09-05)