Releases
v3.2.5
Features
Issue key
Summary
NIR-636
Fix transcripts with translational readthrough (AA difference)
NIR-631
Add support for non-AUG start codons
NIR-627
Fix transcripts with cDNA frameshifts
NIR-625
Fix transcripts with cDNA substitutions
NIR-624
Fix transcripts with missing poly A tails in cDNA
NIR-456
Remove reference bases from HGVS notation
Bugs fixed
Issue key
Summary
NIR-702
Nirvana should stop after inserted terminal codon in HGVS p.
NIR-667
Nirvana is unable to count the # of AA until new stop codon (HGVS p. frameshift)
NIR-666
Nirvana creates frameshift HGVS p. notation when extension is expected
NIR-665
Nirvana uses incorrect HGVS p. notation for disrupted translation initiation codons
NIR-484
Incorrect gene models were found for NM_022148.2
NIR-220
Incorrect HGVS p. results because Nirvana does not use the transcript sequence
NIR-219
Nirvana reports incorrect HGVS p. for non-AUG start codon variants
NIR-57
Nirvana produces bizarre HGVS p. notation (NP_001137434.1:p.(Val701_?_fsTer?))
NIR-55
Nirvana produces invalid CDS positions
Unresolved bugs
Issue key
Summary
Fix Version
NIR-721
Nirvana does not properly preload <NON_REF> variants
3.9.0
NIR-714
Nirvana should trim and LS variants during TopMed lift-over using dbSNP IDs
3.9.0
NIR-719
Nirvana does not remove missing values in 1KG SV IDs
3.8.0
NIR-722
Nirvana does not throw error when annotating unsorted VCF file
3.6.0
NIR-718
Nirvana reports zero allele frequencies for 1KG SV supplementary annotations
3.6.0
NIR-717
Nirvana does not annotate properly when variants fall into transcript gaps
3.5.0
NIR-713
Nirvana cannot handle OMIM phenotype 617956 (β-glucopyranoside tasting)
3.5.0
NIR-720
Nirvana creates empty custom annotations
3.3.0
NIR-716
Nirvana should assign copy_number_loss to <DEL> with SVTYPE=CNV
3.3.0
NIR-715
Nirvana provides extra PhyloP scores for some genomic positions
3.3.0
NIR-712
Nirvana is missing dbSNP annotations for mitochondrial variants
3.3.0
NIR-703
Nirvana incorrectly handles deletions across the terminal codon in HGVS p.
NIR-701
Nirvana should simplify HGVS p. notation for deletions that disrupt the initiation codon
NIR-86
Nirvana should use the transcript sequence for HGVS c. instead of reference
NIR-56
CDS position goes beyond the CDS sequence length (NM_001300952.1)
You can’t perform that action at this time.