recipe hmftools-sage

SAGE is a somatic SNV, MNV and small INDEL caller optimised to call narrow regions of the genome with high prior chance of a variant with very high sensitivity.



GPL / GPL-3.0-only



package hmftools-sage

(downloads) docker_hmftools-sage



depends bioconductor-genomicranges:

depends bioconductor-variantannotation:

depends font-ttf-dejavu:

depends openjdk:


depends r-dplyr:

depends r-ggplot2:

depends r-tidyr:

depends xorg-libxt:

depends zlib:



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 hmftools-sage

and update with::

   mamba update hmftools-sage

To create a new environment, run:

mamba create --name myenvname hmftools-sage

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 `hmftools-sage/tags`_ for valid values for ``<tag>``)

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