Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
 Samtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
 BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
 HTSlib - A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Documentation

Home page
Manuals
Source code

Slurm script

Using the package under srun. A batch script can also be used.

$ module load load samtools
$ samtools view colons.bam
chr1	0	chr1	1	0	10M	*	0	0	AACCGCGGTT	*
chr1b	0	chr1	111	0	10M	*	0	0	AACCGCGGTT	*
chr1:100	0	chr1:100	100	0	10M	*	0	0	AACCGCGGTT	*
chr1:100-200	0	chr1:100-200	100	0	10M	*	0	0	AACCGCGGTT	*
chr2:100-200	0	chr2:100-200	100	0	10M	*	0	0	AACCGCGGTT	*
chr1,chr3	0	chr1,chr3	100	0	10M	*	0	0	AACCGCGGTT	*
$ samtools sort -O bam -o colons_sorted.bam colons.bam