mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra

Abstract

SummaryCharacterization of germline mutation spectrum variation from population genomics data has shed light on the biological complexity of the mutation process, and its evolution within and between species. This analysis augments available population SNP data with estimates of local ancestral genomic context to assign mutation types and aggregate summary statistics thereof, and is increasingly common. There is a need for standardized computational tools to extract mutation spectrum information from sequencing data. Here I describe mutyper, a command-line utility and Python package that uses an ancestral genome estimate to assign mutation types to SNP data, compute mutation spectra for individuals, and compute sample frequency spectra resolved by mutation type for population genetic inference. Availability and implementationmutyper can be installed using the pip package manager and is compatible with Python 3.6+. Documentation is provided at https://harrispopgen.github.io/mutyper; source code is available at https://github.com/harrispopgen/mutyper.