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.

Software Details

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Licence: MIT/Expat License

Application: Bioinformatics

Platform: Linux-64


Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9; Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. Epub 2011 Sep 8; Danecek P., Schiffels S., Durbin R. Multiallelic calling model in bcftools (-m),; Li H. Improving SNP discovery by base alignment quality. Bioinformatics. 2011 Apr 15;27(8):1157-8. doi: 10.1093/bioinformatics/btr076. Epub 2011 Feb 13; , Durbin R. Segregation based metric for variant call QC; Li H, Mathematical Notes on SAMtools Algorithms

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