MCNV2 (Mendelian CNV Validation): Mendelian Precision for CNV quality assessment

Abstract

SummaryDetection of copy number variations from genomic sequencing and array data is prone to high false-positive rates. Distinguishing true variation from false positives remains challenging as quality metrics depend on technologies used, the quality of the data, and the calling algorithm. Mendelian inheritance in parent-offspring trios offers a powerful method to detect false positives, yet no tool exists to systematically compute, explore, optimize, and interpret the precision of CNV calls accordingly. Here we present Mendelian CNV Validation (MCNV2), an R package implementing Mendelian Precision (MP), as a reproducible metric for standardized CNV quality assessment. MCNV2 provides a command-line interface for pipeline integration and an interactive Shiny application for real-time exploration of MP across CNV types, size categories, and quality metrics. Availability and ImplementationMCNV2 is available at https://github.com/JacquemontLab/MCNV2-Mendelian-CNV-Validation. Contactmame.seynabou.diop@umontreal.ca Supplementary InformationSupplementary information are available at https://mcnv2-mendelian-cnv-validation.readthedocs.io/en/latest/