PennCNV 2 20131206
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-2 is the second major release of the popular program PennCNV, which was originally designed for inferring copy number variation in germline DNA using data from genotyping microarrays. PennCNV-2 now supports inference of copy number abberrations in tumor cells (PennCNV-tumor).
- Windows with Cygwin/ Linux / MacOSX
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Bioinformatics. 2013 Dec 1;29(23):2964-70. doi: 10.1093/bioinformatics/btt521. Epub 2013 Sep 9.
Precise inference of copy number alterations in tumor samples from SNP arrays.
Chen GK1, Chang X, Curtis C, Wang K.
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