genoCN 1.09

:: DESCRIPTION

GenoCN is a software that simultaneously identify copy number states and genotype calls. Different strategies are implemented for the study of Copy Number Variations (CNVs) and Copy Number Aberrations (CNAs). While CNVs are naturally occurring and inheritable, CNAs are acquired somatic alterations most often observed in tumor tissues only. CNVs tend to be short and more sparsely located in the genome compared to CNAs. GenoCN consists of two components, genoCNV and genoCNA, designed for CNV and CNA studies, respectively. In contrast to most existing methods, genoCN is more flexible in that the model parameters are estimated from the data instead of being decided a priori. genoCNA also incorporates two important strategies for CNA studies. First, the effects of tissue contamination are explicitly modeled. Second, if SNP arrays are performed for both tumor and normal tissues of one individual, the genotype calls from normal tissue are used to study CNAs in tumor tissue.

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

• Linux/Windows/MacOsX
• R Package
• C Compiler

:: DOWNLOAD

  genoCN

:: MORE INFORMATION

Citation

Sun, W., Wright , F., Tang, Z.Z., Nordgard , S.H., Van Loo, P., Yu, T., Kristensen, V., Perou, C.,
Integrated study of copy number states and genotype calls using high density SNP arrays.
Nucleic Acids Res. 2009, 37(16), 5365-77