Code implementing maximum likelihood assignment of mutations to trees. The method uses an EM method to soft assign mutations to branches and simultaneously estimate branch lengths.
Each mutation is assigned to branch with probability:
P(Mutation has genotype ) ~ P(Read Count | genotype)P(genotype)
Where a given branch implies a genotype and P(genotype) is proportional to branch length. The read counts are modelled using the binomial distribution with up to 4 distinct per sample specific error rates and an assumed VAF=0.5 for variant sites and VAF=0 for wild type sites.
library(devtools)
install_git("https://github.com/NickWilliamsSanger/treemut")browseVignettes(“treemut”)