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- Title
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
- Authors
Kim, Jung; Naqvi, Ammar S; Corbett, Ryan J; Kaufman, Rebecca S; Vaksman, Zalman; Brown, Miguel A; Miller, Daniel P; Phul, Saksham; Geng, Zhuangzhuang; Storm, Phillip B; Resnick, Adam C; Stewart, Douglas R; Rokita, Jo Lynne; Diskin, Sharon J
- 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.
- Subjects
GERM cells; WHOLE genome sequencing; MEDICAL genetics; MOLECULAR pathology; MOLECULAR association; WORKFLOW
- Publication
Bioinformatics, 2024, Vol 40, Issue 3, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btae114