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BCFtools (VCF/BCF file manipulation)

Table of Contents


BCFtools is a set of utiltiies for manipulation of genetic sequence variation data stored in files with Variant Call Format (VCF) or the related Binary Call Format (BCF) formats.  Some of the utilities were formerly available as part of Samtools.  The HTSlib commands tabix, bgzip and htsfile are also included in the package.

See the Software Versions tab for a list of systems on which BCFtools have been installed.

Using BCFtools on Breezy

The BCFtools package has been installed under /global/software/bcftools/bcftools13.  Initialize your environment to run BCFtools with:

module load bcftools/1.3


man bcftools

for documentation for the various utilities provided with the BCFtools package.


bcftools -h

for a brief summary of command line arguments for the bcftools executable.

2015-06-24: Page created.
2016-04-15: Updated to version 1.3 on Breezy.

System Breezy
Version 1.3.1 1.3