- Rewrite CharGer to be Python 3.6+ compatible and Python 2.7 is no longer supported. Most of the options have been renamed and unified.
- Input variants must be normalized and biallelic, and must be annotated by VEP with the recommended parameters. Only VCF format is accepted (
.vcf,.vcf.gz, or.bcf). - ClinVar variant table must be Tabix indexed.
- v0.6.0 results are identical to v0.5.4 except for the conditions listed below:
- ClinVar matching now requires the alternative allele to be identical.
- Add support for vcf files annotated with VEP ≥ 90.
- When present in VEP annotation, gnomAD population frequencies are prioritized over ExAC.
- Fix parsing ClinVar information.
- Fix
parseMacPathogenicity()to handle variants with multiple submitters that receive both benign and pathogenic classifications, but no conflict is reported (i.e.isPathogenic == 1 and isBenign == 1 and isConflicted == 0). - [:pr:`19`] Fix
var.splitHGVScdoesn't consider strand information. Whenoverride = True, the ref and alt for genomic variants will be wrongly changed for minus strand transcripts. Default tooverride = False. - [:pr:`19`] Fix coordinates in
getMacClinVarTSV()to matchreadVCF().