AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification
Jung Kim, Ammar S. Naqvi, Ryan J Corbett, Rebecca Kaufman, Zalman Vaksman, Miguel Brown, Daniel P. Miller, Saksham Phul, Zhuangzhuang Geng, Phillip B. Storm, Adam Resnick, Douglas R. Stewart, Jo Lynne Rokita, Sharon J. Diskin
Abstract
SUMMARY: With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics-Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically focused classification of germline sequence variants in a research setting. AVAILABILITY AND IMPLEMENTATION: AutoGVP is an open source dockerized workflow implemented in R and freely available on GitHub at https://github.com/diskin-lab-chop/AutoGVP.