CHANGES.rst

0.6.0 (unreleased)

Backward-incompatible Changes

• 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.

0.5.4 (2019-09-30)

Changes

• Add support for vcf files annotated with VEP ≥ 90.
• When present in VEP annotation, gnomAD population frequencies are prioritized over ExAC.

0.5.3 (2019-09-30)

Bug Fixes

• 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.splitHGVSc doesn't consider strand information. When override = True, the ref and alt for genomic variants will be wrongly changed for minus strand transcripts. Default to override = False.
• [:pr:`19`] Fix coordinates in getMacClinVarTSV() to match readVCF().