JacquemontLab/CNV-Annotation: v2.0

Release v2.0 This repository, maintained by our lab, provides a reproducible Nextflow pipeline developed by the Jacquemont Lab for the systematic annotation of copy number variants (CNVs). Starting from a single cohort-level CNV TSV file, the pipeline integrates genomic context, gene and transcript disruption, population frequency, constraint metrics, and known recurrent CNVs to produce analysis-ready databases in Parquet format. The workflow is designed for large-scale cohort studies, supports both GRCh37 and GRCh38, and prioritizes canonical and MANE transcripts to balance biological interpretability and database size.