v0.5.4

Added support for vcf files annotated with VEP releases ≥ 90

• Added support for vcf files annotated with VEP releases ≥ 90.
• When present in VEP annotation, CharGer prioritizes gnomAD population frequencies over ExAC.

v0.5.3

Bug fixes in parsing of ClinVar information

Changes include:

• Fixed parseMacPathogenicity() to handle variants with multiple submitters that received both benign and pathogenic classifications, but no conflict is reported (i.e. isPathogenic == 1 and isBenign == 1 and isConflicted == 0)

• Fixed bug reported in pull request #19: var.splitHGVSc, which doesn't consider strand information. When override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts. Changed to override = False

• Fixed bug reported in pull request #19: fixed corrdinates in getMacClinVarTSV() to match readVCF().

New Modules & Scores

The scoring system now includes expert tuned values that we have used in prior projects (previously updated in post-processing). Additionally, custom modules have been added to capture information not considered explicitly by ACMG.

Localized

Local VEP can be used for annotating. Local ExAC .vcf can be used to access allele frequency for each variant. MacArthur's lab has cleaned up the inconsistencies coming from ClinVar's .tsv, .xml, and .vcf downloads. The MacArthur lab output .tsv of ClinVar can be used for known pathogenicity. Each of these will override the BioMine accession that would otherwise go through ReST web interfaces.

2016 - first version

CharGer has been used in a few projects in 2016. This release is or at least is close to the version of the first uses.