Charger

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.

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.

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.