PennCNV / PennCNV-Seq v1.0.5 – Copy Number Variation detection

PennCNV / PennCNV-Seq v1.0.5

:: 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.

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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).

PennCNV-Seq is an adaptation of the original PennCNV algorithm for whole-genome sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / MacOSX
  • Perl

:: DOWNLOAD

 PennCNV ;PennCNV-Seq

:: MORE INFORMATION

Citation

de Araújo Lima L, Wang K.
PennCNV in whole-genome sequencing data.
BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):383. doi: 10.1186/s12859-017-1802-x. PMID: 28984186; PMCID: PMC5629549.

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

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