mutyper: assigning and summarizing mutation types foranalyzing germline mutation spectra

The germline mutation process drives genetic variation and provides the raw material for adaptive evolution.Germline mutations arise from spontaneous DNA damage caused by environmental mutagens, or errors in DNA replication.Populations and species may experience distinct mutational histories due to variation in environmental exposure, life history, and heritable variation in the machinery controlling DNA replication fidelity.Mutational mechanisms often have mutation signatures in terms of the nucleotide sequence contexts where they act.Population genomics has given increasing attention to nucleotide sequence context in the study of the germline mutation process (reviewed in Carlson et al. ( 2020)).Single-nucleotide polymorphisms (SNPs) can be assigned to mutation types by the ancestral and derived nucleotide states and a window of local nucleotide context in the ancestral background.The mutation spectrum of an individual or population is the relative distribution of these mutation types.