ADMIXTURE.jl

Julia wrapper of the ADMIXTURE program for estimating ancestry
Author OpenMendel
Github
Popularity
6 Stars
Updated Last
1 Year Ago
Started In
August 2020

ADMIXTURE.jl

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ADMIXTURE.jl is a Julia wrapper of the popular ADMIXTURE program for estimating ancestry in a model-based manner from large autosomal SNP genotype data sets.

The methodology is described in following papers:

  1. D Alexander, J Novembre, and K Lange. (2009) Fast model-based estimation of ancestry in unrelated individuals, Genome Research, 19(9):1655–1664. https://dx.doi.org/10.1101/gr.094052.109

  2. D Alexander and K Lange. (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics, 12:246. https://doi.org/10.1186/1471-2105-12-246

  3. S Shringarpure, C Bustamante, K Lange, and D Alexander. (2016) Efficient analysis of large datasets and sex bias with ADMIXTURE. BMC Bioinformatics 17:218. https://doi.org/10.1186/s12859-016-1082-x

ADMIXTURE.jl requires Julia v1.3 or later. See documentation for usage. It is not yet registered and can be installed, in the Julia Pkg mode, by

(@v1.5) Pkg> add https://github.com/OpenMendel/ADMIXTURE.jl

The original ADMIXTURE software thus ADMIXTURE.jl only support Linux and MacOS.

As a quick example, suppose a set of PLINK files hapmap3.bed, hapmap3.bim, hapmap3.fam are available in the current directory. Then

P, Q = admixture("hapmap3.bed", 3)

returns the P matrix (allele frequencies of the inferred ancestral populations) and the Q matrix (the ancestry fractions). The output files by ADMIXTURE are saved in the working directory.

For more details, check the documentation.