CFHMM: Heterogeneous Tumor CNV Classification by Hidden Markov.

Summary: We here develop and implement a Clonal Fraction Hidden Markov Model (CFHMM), to leverage positional information in classifying Tumor CNVs and their corresponding clonal fraction from log-ratio-normalized Tumor/Normal sequencing data. In simulated data, this approach shows accurate calling of CNVs for high-fraction mutations, and improvement in calling over a naïve clustering benchmark across the board, as well as useful purity estimation for dominant clones. Availability and Implementation: Source code and documentation is freely available at https://github.com/7lagrange/FCNV implemented in R, with all major operating systems supported. [ABSTRACT FROM AUTHOR]