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.