recipe bamsurgeon

Tools for adding genomic variants to BAM/SAM/CRAM files. Can be used to test variant callers.






package bamsurgeon

(downloads) docker_bamsurgeon



depends bwa:


depends exonerate:


depends picard:

depends pysam:

depends python:


depends samtools:


depends velvet:


depends wgsim:




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 bamsurgeon

and update with::

   mamba update bamsurgeon

To create a new environment, run:

mamba create --name myenvname bamsurgeon

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 `bamsurgeon/tags`_ for valid values for ``<tag>``)

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