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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.

ANGSD

ANGSD (Analysis of Next Generation Sequencing Data) is a program for analysing NGS data. It can estimate many summary statistics and perform population-genetic analyses directly from genotype likelihoods, which makes it well suited to low-coverage sequencing data. It reads BAM/CRAM alignments and other common formats.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 0.940, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load angsd/0.940

ANGSD is run with the angsd command. For example, to calculate genotype likelihoods for a set of BAM files listed in bam.filelist:

angsd -bam bam.filelist -GL 1 -doGlf 2 -doMajorMinor 1 -SNP_pval 1e-6 -out results

ANGSD can use multiple threads with the -nThreads option.

Example batch script

#!/bin/bash
#SBATCH --job-name=angsd
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load angsd/0.940

angsd -bam bam.filelist -GL 1 -doGlf 2 -doMajorMinor 1 -SNP_pval 1e-6 -nThreads $SLURM_CPUS_PER_TASK -out results

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