ANGSD

Introduction

ANGSD is a software for analyzing next generation sequencing data. Detailed usage can be found here: http://www.popgen.dk/angsd/index.php/ANGSD.

Versions

• 0.935

• 0.937

• 0.939

• 0.940

Commands

• angsd

• realSFS

• msToGlf

• thetaStat

• supersim

Module

You can load the modules by:

module load biocontainers
module load angsd/0.937

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run angsd on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=angsd
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers angsd/0.937

angsd -b bam.filelist -GL 1 -doMajorMinor 1 -doMaf 2 -P 5 -minMapQ 30 -minQ 20 -minMaf 0.05