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CNV Calling
Trio Calling
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De novo CNV
Validation Calling
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PennCNV Plug-in
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PennCNV: copy number variation detection

Welcome! PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

Click the menu to the left to navigate through the PennCNV website. If you have questions, comments or concerns, contact

What’s new:

New: Updated PennCNV version (June 2011) can be accessed in the Download page. Only minor bug fixes are included. Additionally, pre-compiled executables are included for 32-bit Perl 5.8.9, 5.10.1, 5.12.3 and 5.14.0 in Windows XP, Vista and 7.

new: User-contributed programs (December 1 , 2010 and Feburary 27, 2011) to convert PennCNV call to PLINK format, and to plot PennCNV rawcnv file on multiple individuals to a high solution PNG file for comparing CNV calls across individuals.

new: Minor changes to in the Download page (August 09 , 2010) to improve graphics (JPG/PDF) production and immitate Illumina GenomeStudio screen shots.

new: A few minor changes to helper scripts can be accessed in the Download page (June 07, 2010).