Skip to main content
An official website of the United States government
Government Funding Lapse
Because of a lapse in government funding, the information on this website may not be up to date, transactions submitted via the website may not be processed, and the agency may not be able to respond to inquiries until appropriations are enacted.

The NIH Clinical Center (the research hospital of NIH) is open. For more details about its operating status, please visit cc.nih.gov.

Updates regarding government operating status and resumption of normal operations can be found at opm.gov.

Email

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.
 

Enlarge Image

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 as well as allows for reproducibility of variant classification. 

Website

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.

If you would like to reproduce some or all of this content, see Reuse of NCI Information for guidance about copyright and permissions. In the case of permitted digital reproduction, please credit the National Cancer Institute as the source and link to the original NCI product using the original product's title; e.g., “Automated Germline Variant Pathogenicity (AutoGVP) was originally published by the National Cancer Institute.”

Email