Additional file 1.
Optional post-processing of CBS segments. Removing splits from CBS as a function of coverage and the standardized difference in segment means. Baum-welch updates Initialization and updating of parameters for the emission distributions. Models for Mendelian transmission of the offspring copy number Details regarding the adaption of the PennCNV probabilistic model of Mendelian transmission. PennCNV annotation for trio copy number states Annotation of trio copy number states in PennCNV. Empirical estimation of simulation parameters in the oral cleft study Estimation of simulation parameters from the oral cleft study Renvironment and software versions
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Scharpf et al. BMC Bioinformatics 2012 13:330 doi:10.1186/1471-2105-13-330