Release 3.15 · Illumina/Nirvana

Features

Issue key	Summary
NIR-574	Update OMIM
NIR-569	Update ClinVar
NIR-540	Add command-line arguments to the Downloader for changing S3 URLs and manifest filenames
NIR-520	Add support for identifying in-frame gene fusions
NIR-495	Port bidirectional allele trimmer fix for breakend locations when using legacy VID mode
NIR-494	Port legacy VID fixes from 3.6.x
NIR-480	Add support for INV3/INV5 tags with respect to gene fusions
NIR-477	Add support for FusionCatcher data sources
NIR-474	Add support for COSMIC gene fusions
NIR-459	Update HGVS g. notation for MT variants to use m. notation
NIR-324	Allow masked reference bases in PAR regions (chrY)
NIR-257	Update Nirvana to use gnomAD 3.1 for GRCh38
NIR-250	Update the BlockCompression library
NIR-193	Add support for detecting out of disk space issues in Downloader

Issue key	Summary
NIR-548	Nirvana incorrectly recomposes an deletion and assigns a negative genotype
NIR-398	Mito Heteroplasmy not using trimmed and left-aligned alt alleles for annotation
NIR-214	Nirvana doesn't support regular gzip VCF file
NIR-213	Downloader unintentionally removes genomic reference file

Issue key	Summary
NIR-602	SAUtils CustomVar won't allow missing values for Score columns
NIR-582	Jasix incorrectly closes the JSON header when combining query with header
NIR-504	SingleAnnotation behaves differently in Lambda vs REST API
NIR-220	Nirvana doesn't use the transcript sequence to report the reference amino acids in HGVS p. notations
NIR-219	Nirvana reports ambiguous protein level annotations for CUG start codon variants
NIR-218	Duplicates may be marked as insertions in HGVS
NIR-217	Nirvana produces HGVS insertions notations that are more than one bp apart
NIR-215	Nirvana incorrectly determines gnomAD low complexity regions at translocation breakend boundaries
NIR-212	Annotation lambdas run out of disk space when large amounts of CA are submitted
NIR-91	Nirvana should fully right align duplications in HGVS c. notation
NIR-87	Nirvana should detect duplications in HGVS by looking at the transcript sequence.
NIR-86	Nirvana incorrectly handles insertions where RNA-edit insertions already occur
NIR-75	Nirvana doesn't handle 3' UTR intron HGVS c. notation properly
NIR-57	Nirvana produces bizarre HGVS p. notation (NP_001137434.1:p.(Val701_?_fsTer?))
NIR-56	CDS position goes beyond the CDS sequence length (NM_001300952.1)
NIR-55	Nirvana produces a strange CDS position range for NM_001346067.1