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. In addition to case-control studies, 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:
: Updated PFB file available to handle HumanHap1M-Duo and HumanHap660W arrays in the Download page (April 2009) . : Patch available to fix gender prediction issue on chrX CNV calling for Affymetrix arrays in the Download page (January 2009) . : Updated PennCNV version (November 2008) can be accessed in the Download page. : The PennCNV-Affy protocol for Affymetrix arrays can be accessed in the PennCNV-Affy page.: The Genome Browser track for markers on commonly used SNP arrays can be accessed in the Download page. : Join PennCNV mailing list for program update and announcement in the Mailing List page.Reference:
- Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data Genome Research 17:1665-1674, 2007
- Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms Nucleic Acids Research 36:e126, 2008
- Wang K, Chen Z, Tadesse MG, Glessner J, Grant SFA, Hakonarson H, Bucan M, Li M. Modeling genetic inheritance of copy number variations Nucleic Acids Research 36:e138, 2008