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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

AdmixTools

AdmixTools is a package for inferring population history and admixture from genome-wide allele-frequency data using f-statistics. It provides a set of command-line programs, including qpDstat (D-statistics), qp3Pop (f3-statistics), qpAdm and qpGraph (admixture modelling), qpF4ratio (admixture proportions) and convertf (file-format conversion).

License

AdmixTools may be freely copied for non-commercial purposes, provided the upstream copyright notice is retained. See the AdmixTools README for licensing terms.

Available

  • Roihu: 8.0.2, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load admixtools/8.0.2

The AdmixTools programs are driven by a parameter file that lists the input files and options. For example, a D-statistics analysis is run with:

qpDstat -p parfile > qpDstat.log

See the AdmixTools documentation for the parameter-file format and options of each program.

Longer analyses should be run as batch jobs. Below is a simple example batch job script:

#!/bin/bash
#SBATCH --job-name=admixtools
#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=1
#SBATCH --mem=8G

module load bio-apps/v202603
module load admixtools/8.0.2

qpDstat -p parfile > qpDstat.log

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

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