• 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

Version: 1.2 – Visit their website and view the support site

Licence: MIT/Expat License

Application: Bioinformatics

Platform: Linux-64

Last Updated: May 13, 2015

Citation:

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. [PMID: 19505943]

* 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. [PMID: 21903627]

* Danecek P., Schiffels S., Durbin R. Multiallelic calling model in bcftools (-m), samtools.github.io/bcftools/call-m.pdf

* 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. [PMID: 21320865]

* Durbin R. Segregation based metric for variant call QC, samtools.github.io/bcftools/rd-SegBias.pdf

* Li H, Mathematical Notes on SAMtools Algorithms, www.broadinstitute.org/gatk/media/docs/Samtools.pdf

If you wish to use a different version of a program, or to request an upgrade to a newer version of existing software, please submit your request here.