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BCFtools

  • Description

    a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

  • Usage

    To list all executables provided by BCFtools, run: $ sbgrid-list bcftools Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install bcftools Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    H. Li. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 27(21): 2987-2993.

    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

    Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008

  • Keywords

    High-throughput sequencing, WGS Analysis

  • Default Versions

    Linux 64:  1.19 (50.5 MB)
    OS X INTEL:  1.19 (82.1 MB)

  • Other Versions

      Linux 64:

      1.10.2 (29.2 MB) , 1.12 (390.0 MB) , 1.16 (1.5 GB) , 1.17 (49.0 MB) , 1.18 (49.0 MB) , 1.3 (4.4 MB) , 1.3.1 (4.5 MB) , 1.6 (87.9 MB)

    • OS X INTEL:

      1.10.2 (3.1 MB) , 1.12 (3.2 MB) , 1.16 (3.5 MB) , 1.17 (80.7 MB) , 1.18 (81.2 MB) , 1.3 (1.5 MB) , 1.3.1 (1.5 MB) , 1.6 (38.6 MB)

  • Developers

    Heng Li, John Marshall, Petr Danecek, Shane McCarthy

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