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:
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:
- git clone git://github.com/samtools/htslib.git
- git clone git://github.com/samtools/bcftools.git
- cd bcftools
- # The following is optional:
autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters
- cd htslib; git pull
- cd ../bcftools; git pull
- make clean
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