PennCNV¶

Description¶

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.

Environment Modules¶

Run module spider penncnv to find out what environment modules are available for this application.

Environment Variables¶

HPC_PENNCNV_DIR - installation directory
HPC_PENNCNV_BIN - executable directory
HPC_PENNCNV_DOC - documentation directory
HPC_PENNCNV_EXE - examples directory

Citation¶

If you publish research that uses penncnv you have to cite it as follows:

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

Categories¶

phylogenetics