recipe bcftools

BCFtools is 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. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.







biotools: bcftools, usegalaxy-eu: bcftools_merge, doi: 10.1093/bioinformatics/btp352

package bcftools

(downloads) docker_bcftools



depends gsl:


depends htslib:


depends libgcc-ng:


depends libzlib:


depends perl:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bcftools

and update with::

   mamba update bcftools

To create a new environment, run:

mamba create --name myenvname bcftools

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bcftools/tags`_ for valid values for ``<tag>``)

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