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Automated Germline Variant Pathogenicity (AutoGVP)

Flow diagram of AutoGVP. (A) Required input files for custom or CAVATICA workflow. (B) Variant classification method decision tree. (C) Alluvial plot showing how InterVar classification changes in AutoGVP.

Flow diagram of AutoGVP. (A) Required input files for custom or CAVATICA workflow. (B) Variant classification method decision tree. (C) Alluvial plot showing how InterVar classification changes in AutoGVP. The large numbers of concordant VUS (357 656), LB (20 374), and B (28 310) variants were removed for easier visualization. Numbers in parentheses represent the number of variants in that classification. Panels (A) and (B) created with BioRender.com.
 

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Automated Germline Variant Pathogenicity (AutoGVP) integrates ClinVar variant annotation with a modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology (ACMG-AMP) guidelines, to output germline variant classification. Since AutoGVP input only requires a VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants.  

Using automated germline classification reduces hands-on time and allows for reproducibility of variant classification. 

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AutoGVP is an open source, dockerized workflow implemented in R and freely available on GitHub.

Access AutoGVP enabled for Biowulf (on GitHub).

Support

Contact:  Jung Kim 

Reference

Kim J et al. AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification. Bioinformatics. 2024.

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