Overview

MCNV2 (Mendelian CNV Validation) is a framework designed to assess the quality of copy number variations (CNVs) using family-based Mendelian inheritance in parent–offspring trios.

MCNV2 is designed for: - Researchers optimizing CNV calling pipelines (WGS/WES/arrays) - Bioinformatics pipelines that require reproducible QC summaries - Clinical and research labs comparing callers or thresholds

Key idea

True de novo CNVs are rare (1.92%), so most CNVs observed only in offspring are enriched for technical false positives.
MCNV2 leverages this signal to compute Mendelian Precision (MP) without requiring an external benchmark callset.

What MCNV2 provides

  • CLI for automated analyses (pipeline integration, large cohorts)

  • Shiny app for interactive exploration (filters + plots + exports)

  • Annotation modules:

    • gene overlap

    • gene constraint (LOEUF; gnomAD)

    • problematic regions (UCSC tracks: segdups, centromeres, telomeres, HLA)

  • Inheritance modes

    • CNV-level (reciprocal overlap threshold)

    • gene-level (shared affected genes, robust to breakpoint noise)

  • Exports

    • MP summary tables

    • candidate de novo / Mendelian errors lists