lanctools 0.1.3

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lanctools

Tools 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

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

Installation

pip install lanctools

Quickstart

Querying Local Ancestry Data

import numpy as np
from lanctools import LancData

ld = LancData(
    plink_prefix="chr1",
    lanc_file="chr1.lanc",
    ancestries=["YRI", "CEU"]
)

idx_var = np.arange(100, dtype=np.uint32)

# Get phased local ancestry: shape (N, 100, 2)
lanc = ld.get_lanc(idx_var)

# Get phased genotypes: shape (N, 100, 2)
geno = ld.get_geno(idx_var)

# Get ancestry-masked genotypes: shape (N, 100, len(ancestries))
lanc_geno = ld.get_lanc_geno(idx_var)

Converting FLARE or RFMix Files to .lanc

from lanctools import convert_to_lanc

convert_to_lanc(
    file="chr1.anc.vcf.gz",
    file_fmt="FLARE",
    plink_prefix="chr1",
    output="chr1.lanc"
)

Command-Line Interface

lanctools convert-flare --file chr1.anc.vcf.gz --plink_prefix chr1 --output chr1.lanc

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