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).

AdmixTools
- License
- Available
- Usage
- Support
- More information

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

More information

AdmixTools GitHub repository