Genomic alterations associated with disease, such as certain copy number variants (CNVs, also known as copy number alterations, or CNAs), can be very challenging to accurately quantify. These variants, in which specific genomic regions are either deleted or repeated—sometimes hundreds of times—can be associated with many diseases, including cancer, cardiovascular disease, and neurodevelopmental disorders (Pös et al., 2021). For many disease-associated CNVs, accurate CNV counts are essential for understanding their potential biological impact (Steele et al., 2022).