PennCNV: copy number variation detection

Tutorial

• Quick Examples

• Input Files

• CNV Calling

• Trio Calling

• Joint Calling

• De novo CNV

• Validation Calling

• QC & Annotation

• Visualization

• PennCNV Plug-in

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:

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

: Updated PennCNV version (May 2010) can be accessed in the Download page. Changes include: (1) Reduce memory usage (in a 64-bit Linux computer, Affymetrix 6 calling requires ~1.8GB now, compared to ~4GB before). (2) Functionality to automatically plot all CNV calls as JPG files for visual examination. (3) Program to compile custom PFB files from a list of signal intensity files. (4) solved compilation issues on certain systems for the genomic wave adjustment procedure.
: 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