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Updated: Feb 7, 2026

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Identification of Copy Number Variants from SNP Arrays Using PennCNV
1Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Abstract:
High-resolution single-nucleotide polymorphism (SNP) genotyping arrays offer a sensitive and affordable method for genome-wide detection of copy number variants (CNVs). PennCNV is a hidden Markov model (HMM)-based CNV caller for SNP arrays, first released 10 years ago. A typical CNV calling procedure using PennCNV includes preparation of input files, CNV calling, filtering CNV calls, CNV annotation, and CNV visualization. Here we describe several protocols for CNV calling using PennCNV, together with descriptions on several recent improvements to the software tool.
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