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 HSTlib so they can be built independently.