v3.18.1

Features

Issue key	Summary
NIR-1003	Update ClinGen Dosage Sensitivity Map
NIR-1002	Update ClinGen Gene Disease Validity
NIR-1001	Update dbSNP to v155
NIR-1000	Update OMIM to May 2022
NIR-999	Update ClinVar to May 2022
NIR-969	Add DECIPHER SVs to Nirvana
NIR-926	Remove Variant recomposition

Bugs Fixed

Issue key	Summary
NIR-1038	Nirvana displays confusing error message if idx files for gsa files are absent
NIR-1014	Downloader is not using new SA manifest architecture
NIR-996	Nirvana returns duplicate VCVs in ClinVar
NIR-976	Jasix crashes if range is out of the range in the file

Unresolved Bugs

Issue key	Summary
NIR-919	Nirvana does not handle protein sequences that are partially aligned to the genome
NIR-918	Nirvana does not handle ribosomal frameshifts properly during translation
NIR-917	Nirvana does not truncate deletions that start within a deletion RNA-edit (HGVS c.)
NIR-916	Nirvana does not detect HGVS c. duplications when inserting a base into a deletion RNA-edit
NIR-915	Nirvana does not convert SNVs that land in a deletion RNA-edit as an insertion (HGVS c.)
NIR-909	Nirvana Lambda throws Nirvana error if input VCF is not BGZipped
NIR-701	Nirvana should simplify HGVS p. notation for deletions that disrupt the initiation codon
NIR-702	Nirvana should stop after inserted terminal codon in HGVS p.
NIR-703	Nirvana incorrectly handles deletions across the 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-602	SAUtils CustomVar won't allow missing values for Score columns
NIR-504	SingleAnnotation behaves differently in Lambda vs REST API
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-215	Nirvana incorrectly determines gnomAD low complexity regions at translocation breakend boundaries
NIR-86	Nirvana incorrectly handles insertions where RNA-edit insertions already occur
NIR-56	CDS position goes beyond the CDS sequence length (NM_001300952.1)