Variant Call Format–Diagnostic Annotation and Reporting Tool: A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data

Miles C. Benton, Robert A. Smith, Larisa M. Haupt, Heidi G. Sutherland, Paul J. Dunn, Cassie L. Albury, Neven Maksemous, Rodney Lea, Lyn Griffiths*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Abstract

In this article, we introduce the variant call format–diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them on the basis of standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators. The tool uses publicly available databases to identify a range of data to assist with variant classification and curation processes and includes robust logging of parameters and database versions to allow comparison of analyses performed at different times. VCF-DART—an online analysis pipeline for next-generation sequencing data—is a platform agnostic tool that leverages the use of publicly available databases to improve a laboratory's calling ability and reduce analysis times long-term. It also runs highly efficiently and scales from desk and laptop machines to servers. Overall, VCF-DART provides a simple, customizable, and entirely open-source method to identify genetic variants that may be of clinical importance in a variety of genetically important conditions.

Original languageEnglish
Pages (from-to)951-960
Number of pages10
JournalJournal of Molecular Diagnostics
Volume21
Issue number6
DOIs
Publication statusPublished - Nov 2019
Externally publishedYes

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