nf-cavalier: A Nextflow Pipeline for Rare Disease Variant Prioritization and Reporting

Abstract

nf-cavalier is a Nextflow pipeline that automates genomic variant annotation, filtering, and reporting for individuals with rare Mendelian diseases. The pipeline takes as input variant callsets for an individual, family, or rare disease cohort, together with a target gene panel or a phenotype of interest. Variants are then filtered using various customisable criteria, including predicted gene consequence, computational pathogenicity predictions, population frequency, and familial segregation. The sequencing data for candidate variants is then visualised for human review. Candidate variant results are returned in user-friendly output formats, including interactive HTML reports and PowerPoint slide decks, with embedded links to external resources that enable rapid review by clinical research teams. nf-cavalier is maintained on GitHub (bahlolab/nf-cavalier) and licensed under the permissive MIT open-source licence.