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SAMtools

  • 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

    To list all executables provided by SAMtools, run: $ sbgrid-list samtools Copy to clipboard

  • 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 Available operating systems: Linux 64, OS X INTEL

  • 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

  • Keywords

    ChIP-Sequencing, DNA-Sequencing, High-throughput sequencing, RNA-Sequencing, WGS Analysis

  • Default Versions

    Linux 64:  1.21 (578.6 MB)
    OS X INTEL:  1.21 (36.9 MB)

  • Other Versions

      Linux 64:

      0.1.19 (3.6 MB) , 1.10 (10.4 MB) , 1.12 (1.2 GB) , 1.13 (534.7 MB) , 1.14 (814.0 MB) , 1.15 (377.6 MB) , 1.15.1 (180.7 MB) , 1.16 (91.1 MB) , 1.16.1 (91.1 MB) , 1.17 (91.4 MB) , 1.18 (91.4 MB) , 1.19.2 (3.3 MB) , 1.20 (26.4 MB) , 1.3 (3.6 MB) , 1.3.1 (3.6 MB) , 1.4.1 (16.2 MB) , 1.5 (22.9 MB) , 1.6 (98.3 MB) , 1.7 (16.4 MB) , 1.8 (6.5 MB) , 1.9 (7.0 MB)

    • OS X INTEL:

      0.1.19 (1.9 MB) , 1.10 (1.8 MB) , 1.12 (387.3 MB) , 1.13 (39.4 MB) , 1.14 (41.4 MB) , 1.15 (36.8 MB) , 1.15.1 (36.8 MB) , 1.16 (36.9 MB) , 1.16.1 (36.9 MB) , 1.17 (37.1 MB) , 1.18 (3.1 MB) , 1.19.2 (3.2 MB) , 1.20 (2.5 MB) , 1.3 (1.2 MB) , 1.3.1 (1.3 MB) , 1.4.1 (6.2 MB) , 1.5 (10.8 MB) , 1.6 (3.4 MB) , 1.7 (1.5 MB) , 1.8 (1.5 MB) , 1.9 (2.4 MB)

  • Developers

    Bob Handshaker, Heng Li, Petr Danecek

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