samtools
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'samtools' Versions
- 1.15
- 1.16
- 1.17
- 1.9
Link to section 'Commands' of 'samtools' Commands
- samtools
- ace2sam
- htsfile
- maq2sam-long
- maq2sam-short
- tabix
- wgsim
Link to section 'Module' of 'samtools' Module
You can load the modules by:
module load biocontainers
module load samtools
Link to section 'Example job' of 'samtools' 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 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
samtools sort my.sam > my_sorted.bam
samtools index my_sorted.bam