ADMIXTURE

Overview

Used to estimate individual ancestry from single nucleotide polymorphism (SNP) data sets.

Availability

Cluster	Module/Version
BOSE	admixture/1.3.0
BGSC	admixture/1.3.0

Note: You can simply use module load admixture to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the admixture command that we wanted to highlight. See Resources for more.

Option	Description
--help	displays the help page
-j#	use # number of thread. Using `$SLURM_NTASKS` is recommended as your value instead of manually specifying a number.

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load admixture    # Load ADMIXTURE
admixture -j${SLURM_NTASKS} hapmap3.bed 3

Real Example

Has your research group used ADMIXTURE in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of ADMIXTURE.

D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.

The developers also shared a citation for the quasi-Newton convergence method.

H. Zhou, D. H. Alexander, and K. Lange. A quasi-Newton method for accelerating the convergence of iterative optimization algorithms. Statistics and Computing, 2009.