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ADMIXTURE

ADMIXTURE is a tool for fast maximum-likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but computes estimates much faster using a numerical optimization algorithm.

License

ADMIXTURE is free to use. It is distributed as a binary; see the ADMIXTURE home page for the license terms.

Available

  • Roihu: 1.4.0, via the bio-apps module.

Usage

ADMIXTURE is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the ADMIXTURE module:

module load bio-apps/v202603
module load admixture/1.4.0

ADMIXTURE takes a PLINK .bed (or .ped) genotype file and the number of assumed ancestral populations K. For example, to run with K = 3:

admixture input.bed 3

This produces the ancestry fractions (input.3.Q) and allele frequencies (input.3.P). ADMIXTURE can use multiple threads with the -j option.

Example batch script

#!/bin/bash
#SBATCH --job-name=admixture
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load admixture/1.4.0

admixture -j$SLURM_CPUS_PER_TASK input.bed 3

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information