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

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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Credits

Author: Franklin Ockerman

License

MIT

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Python >=3.10

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1.0.3 This release

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1.0.2

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1.0.1

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1.0.0

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0.4.0

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0.3.0

21 files

0.2.0

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0.1.4

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0.1.3

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0.1.2

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0.1.1

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0.1.0

22 files

0.0.0

2 files

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