Bcftools

Manual page
Documentation
VCF/BCF/BAM encryption

View the Project on GitHub samtools/bcftools
Download www.htslib.org

This is the official development repository for BCFtools. It contains all the "vcf..." commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools. BCFtools are meant as a faster replacement for most of the perl VCFtools commands.

Download and compiling

The latest release can be downloaded from www.htslib.org.

The most up to date (development) version of BCFtools can be obtained from github using these commands:

git clone git://github.com/samtools/htslib.git
git clone git://github.com/samtools/bcftools.git
cd bcftools; make

The clone command above is used to create a local copy of the remote repository and needs to be run only once. Whenever the latest snapshot from github is needed, use instead the pull command:

cd htslib; git pull
cd ../bcftools; git pull
make clean
make

IMPORTANT
In order to use the BCFtools plugins, this environment variable must be set and point to the correct location:

export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins

Bcftools

Download and compiling

Methods

See also