Samtools

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.

Download

Source code releases can be downloaded from Sourceforge:

Get source releases

Workflows

We have described some standard workflows using Samtools: