Release 3.2.5.1 · Illumina/Nirvana

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

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

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)