3.14

Features

Issue key	Summary
NIR-210	Cap VRF to 0.999

Bugs fixed

Unresolved bugs

Issue key	Summary
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-216	Nirvana reports extra ClinVar SNVs where there is no alternate allele in XML source file
NIR-215	Nirvana incorrectly determines gnomAD low complexity regions at translocation breakend boundaries
NIR-214	Nirvana doesn't support regular gzip VCF file
NIR-213	Downloader unintentionally removes genomic reference file
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