Introduction - If you have any usage issues, please Google them yourself
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtoolsReading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlibA 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.