mutyper

mutyper annotates biallelic single nucleotide polymorphisms (SNPs) with local ancestral genomic context to assign mutation types and compute mutation spectra and sample frequency spectra for population-genomic analyses.

Key Features:

• Ancestral Context Annotation: Augments population SNP data with estimates of local ancestral genomic context at each site.
• Mutation Type Assignment: Assigns specific mutation types to biallelic SNPs using an estimated ancestral genome.
• Computation of Mutation Spectra: Computes per-individual mutation spectra and sample frequency spectra resolved by mutation type.
• Interoperability with MUSHI: Produces outputs compatible with MUSHI (Mutation Spectrum History Inference) for mutation spectrum history analyses.

Scientific Applications:

• Population Genomics: Enables analysis of genetic diversity and evolutionary patterns across populations using mutation-type-resolved spectra and frequency spectra.
• Genetic Epidemiology: Supports investigation of the genetic basis and hereditary transmission of disease by resolving mutation types in population SNP data.
• Evolutionary Biology: Facilitates study of mutation processes, species divergence, and adaptation through mutation-type-resolved analyses.

Methodology:

Annotates biallelic SNPs using an ancestral genome estimate to infer local ancestral genomic context, assigns mutation types, and computes per-individual mutation spectra and sample frequency spectra resolved by mutation type.