Ancestral \(k\)-mer Mutation Types for SNP Data
mutyper is a command line utility and Python package for augmenting genomic variation data in VCF/BCF format with information about the local ancestral sequence context of each variant.
Studying mutation spectra usually begins with computing the mutation type for SNPs in a VCF/BCF file.
To polarize SNPs from REF/ALT to ancestral/derived and determine their local context, we need an estimate of the ancestral sequence, which usually takes the form of a FASTA file.
The mutyper command-line interface makes it easy to include such analysis in more complex bioinformatic pipelines.
The Python API can be used for exploratory mutation type analysis in Python scripts or Jupyter notebooks.
User Guide
API
Developer
Notes