Samtools is by far a very rich software program that provides many different sets of utilities to process high throughput sequence data. This example page would not be possible to cover all of them, but only serve as a sample/template of how to use it on SCC.
Samtools consists of three separate parts:
Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
A C library for reading/writing high-throughput sequencing data