BACOM (Bayesian Analysis of COpy number Mixtures) is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, through which users can smoothly incorporate BACOM into their specific analyses.
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BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.
Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.
Bioinformatics. 2011 Jun 1;27(11):1473-80. Epub 2011 Apr 15.