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AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification
Jung Kim1, Ammar S Naqvi2,3, Ryan J Corbett2,3
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States.
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.
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