polyHap is a tool to phase and estimate missing genotypes in copy number variable (CNV) regions. The polyHap algorithm uses a hidden Markov model (HMM).
Su SY, White J, Balding DJ, Coin LJ "Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions." BMC Bioinformatics. 2008 Dec 1;9:513. https://doi.org/10.1186/1471-2105-9-513
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