AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

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 htt

SUBMITTER: Kim J 

PROVIDER: S-EPMC10955249 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature