Angsd

Introduction

Angsd is a software for analyzing next generation sequencing data.

For more information, please check:

Home page: http://www.popgen.dk/angsd/index.php/ANGSD

Versions

• 0.939

• 0.940

Commands

• angsd

• realSFS

• msToGlf

• thetaStat

• supersim

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 clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=angsd
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load angsd/XXXX ### you can run module avail angsd to check all available versions

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