Samtools
Introduction
Samtools
is a set of utilities for the Sequence Alignment/Map (SAM) format.
For more information, please check its website: https://biocontainers.pro/tools/samtools and its home page on Github.
Versions
1.15
1.16
1.17
1.9
Commands
samtools
ace2sam
htsfile
maq2sam-long
maq2sam-short
tabix
wgsim
Module
You can load the modules by:
module load biocontainers
module load samtools
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 Samtools on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=samtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers samtools