recipe smcounter2

smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers






package smcounter2

(downloads) docker_smcounter2



depends bedtools:

depends openpyxl:

depends pysam:

depends python:


depends r-base:

depends r-plyr:

depends scipy:

depends statistics:



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 smcounter2

and update with::

   mamba update smcounter2

To create a new environment, run:

mamba create --name myenvname smcounter2

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 `smcounter2/tags`_ for valid values for ``<tag>``)

Download stats