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.

• ANGSD
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• ANGSD home page
• ANGSD GitHub repository

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