recipe mantis-msi2

MANTIS2 is a program developed for detecting microsatellite instability from paired-end BAM files






MANTIS2 (Microsatellite Analysis for Normal-Tumor InStability) is a program developed for detecting microsatellite instability from paired-end BAM files. To perform analysis, the program needs a tumor BAM and a matched normal BAM file (produced using the same pipeline) to determine the instability score between the two samples within the pair. Longer reads (ideally, 100 bp or longer) are recommended, as shorter reads are unlikely to entirely cover the microsatellite loci, and will be discarded after failing the quality control filters. Originally developed and maintained here:

package mantis-msi2

(downloads) docker_mantis-msi2



depends libgcc-ng:


depends libstdcxx-ng:


depends numpy:


depends pysam:


depends python:




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 mantis-msi2

and update with::

   mamba update mantis-msi2

To create a new environment, run:

mamba create --name myenvname mantis-msi2

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 `mantis-msi2/tags`_ for valid values for ``<tag>``)

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