This repository is an archive for the bioinformatic code required to reproduce the evolutionary modeling and clone-based WGS data analyses presented in Schratz et al. (TBD).
Snakemake pipeline used for processing of clone-based WGS data to generate somatic phylogenies. An additional readme is available for a full description of the pipeline.
Rmarkdown notebook detailing the methods used to estimate the probability of recurrent mutation (≥ 2 mutation events) in a population of hematopoietic progenitors given empirical estimates for
Rmarkdown notebook detailing the methods for performing stochastic character mapping to infer the evolutionary origin of a somatic mutation given a phylogenetic tree.
Rmarkdown notebook describing simulations of TERTp somatic evolution in HSPC populations, and code for running simulations and plotting output.