Samtools
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
Description
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.
Note: This page does not cover all features of SAMtools. Please refer to http://www.htslib.org/doc/samtools.html for the complete list of all subtools.