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AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
- Source :
-
Bioinformatics . Mar2024, Vol. 40 Issue 3, p1-4. 4p. - Publication Year :
- 2024
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 13674803
- Volume :
- 40
- Issue :
- 3
- Database :
- Academic Search Index
- Journal :
- Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 176301111
- Full Text :
- https://doi.org/10.1093/bioinformatics/btae114