polyHap is a program for phasing polyploids and copy number regions. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences.
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Bioinformatics. 2010 Jun 1;26(11):1437-45. doi: 10.1093/bioinformatics/btq157. Epub 2010 Apr 20.
Inferring combined CNV/SNP haplotypes from genotype data.
Su SY1, Asher JE, Jarvelin MR, Froguel P, Blakemore AI, Balding DJ, Coin LJ.
Shu-Yi Su et al.
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
BMC Bioinformatics 2008, 9:513