angsd
ANGSD is a software for analyzing next generation sequencing data. Detailed usage can be found here: http://www.popgen.dk/angsd/index.php/ANGSD.
Link to section 'Versions' of 'angsd' Versions
- 0.935
- 0.937
- 0.939
- 0.940
Link to section 'Commands' of 'angsd' Commands
- angsd
- realSFS
- msToGlf
- thetaStat
- supersim
Link to section 'Module' of 'angsd' Module
You can load the modules by:
module load biocontainers
module load angsd/0.937
Link to section 'Example job' of 'angsd' Example job
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