Tools for working with phased local ancestry data stored in the `.lanc` file format

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  • License: MIT
  • Author: Franklin Ockerman
  • Requires: Python >=3.10
  • Provides-Extra: dev , docs
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Project description

lanctools is a python package and command-line tool for working with phased local ancestry data stored in the .lanc file format, as defined by Admix-kit [Hou et al., 2024].

lanctools is designed to provide fast local ancestry queries and convenient conversion from external formats (e.g., FLARE [Browning et al., 2023] and RFMix [Maples et al., 2013]). It focuses on efficient access to .lanc data and is not intended to replace the full functionality of Admix-kit. Features include:

  • Efficient random access to phased local ancestry data
  • Local ancestry-masked genotype queries
  • Conversion from FLARE and RFMix output to .lanc format
  • Merging .lanc files
  • Python API and command-line interface (CLI)

Full documentation can be found here

Development Status

This project is in early development and is only intended for academic use.

Per semantic versioning conventions, anything may change at any time. The API should not be considered stable, and breaking changes may occur without notice.

References

  • Hou, K. et al. Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. Bioinformatics 40, btae148 (2024). paper software
  • Browning, S. R., Waples, R. K. & Browning, B. L. Fast, accurate local ancestry inference with FLARE. Am J Hum Genet 110, 326–335 (2023). paper software
  • Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D. RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. Am J Hum Genet 93, 278–288 (2013). paper software

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