pave v1.6 release candidate 1
Pre-release
Pre-release
charlesshale
released this
03 Jan 00:20
·
2428 commits
to master
since this release
Functional:
- keep splice effect for any phased variants
- HGVS coding for dups now shift position to duplicated bases
- handle phased missense and synonymous protein impacts
- phasing check for SNV/MNV overlap with inframe INDEL separately from frameshift count 2+
- favour protein duplications over inserts when considering realignment
- use stop-gained in HGVS protein instead of frameshift if has both
Bugs:
- check ref codon bases are valid in phasing routine, could cause crash if variant was at very end of exon with open reading frame
- fixed ref codon addition for overlaps in phasing logic
Technical:
- exit on thead error
- multi-threaded
Config:
- threads (default 1)
- removed gnomad_load_chr_on_demand