Supported Applications


  • Description

    (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

  • Usage Notes

    New samtools versions occasionally provide new features, remove older features or change options.

    New versions of samtools are always made the default version in BioGrids/SBGrid.

    For this reason, samtools versions should be explicitly set with a BioGrids/SBGrid version variable:

    export SAMTOOLS=1.15

    This ensures your workflows will continue to use the same version of samtools.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install samtools Copy to clipboard
  • Primary Citation*

    H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000-Genome-Project-Data-Processing-Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16): 2078-2079.

    P. Danecek, J. K. Bonfield, J. Liddle, J. Marshall, V. Ohan, M. O. Pollard, A. Whitwham, T. Keane, S. A. McCarthy, R. M. Davies, and H. Li. 2021. Twelve years of SAMtools and BCFtools. Gigascience. 10(2): giab008.

    • *Full citation information available through

  • Citation Note

    Additional citation information can be found in the publication section of the SAMtools documentation page.

  • Keywords

    DNA-Sequencing, RNA-Sequencing, Utilities

  • Default Versions

    Linux 64:  1.15.1
    OS X INTEL:  1.15.1

  • Other Versions

      Linux 64:

      1.9, 1.8, 1.7, 1.6, 1.5, 1.4.1, 1.3.1, 1.3, 1.15, 1.14, 1.13, 1.12, 1.10, 0.1.19
    • OS X INTEL:

      1.9, 1.8, 1.7, 1.6, 1.5, 1.4.1, 1.3.1, 1.3, 1.15, 1.14, 1.13, 1.12, 1.10, 0.1.19
  • Developers

    Bob Handshaker, Heng Li