VEP98.3 + custom panel

• moved panel_id to optional argument
• added ability to analyze custom panels (BED file with gene symbols)

ClinVar fix + VEP 98

v0.5.1

0.5.1 release

VEP update + germline biomarkers

• General improvements (ACMG classifications)
• Addition of germline biomarkers from CIViC
• Improved interactive filtering (ClinVar)

PCGR updates

v0.4.1

0.4.1 release

Bundle update + restructured report

• Restructured, simplified report
• Data bundle update (ClinVar)
• Users may limit report results through virtual gene panels
• Re-implementation of ACMG classification of novel variants

Bundle update and minor bug fixes

v0.3.0

0.3.0 release

Bundle update and improved ACMG implementations

v0.2.1

updated README

ACMG classification adjustments

• Mechanisms of disease for cancer susceptibility genes (GoF vs. LoF) retrieved from Maxwell et al., Am J Hum Genet, 2016
• Exceptions for HFE/SERPINA1 wrt. high population MAF (BA1)
• Threshold for genes with "primarily truncations" set to 90% pathogenic truncations (BP1)
• Consider only pathogenic ClinVar variants (not likely pathogenic) when checking for novel peptide changes at pathogenic loci (PS1/PM5)

ACMG classification transparency

• Added documentation of ACMG evidence support pr. unclassified variant

Initial release of CPSR

• Pre-release of Cancer Sequencing Predisposition Reporter
• VEP v94 / ClinVar / GWAS catalog / dbNSFP