- 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: https://github.com/OSU-SRLab/MANTIS.
- package mantis-msi2¶
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
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/mantis-msi2:<tag> (see `mantis-msi2/tags`_ for valid values for ``<tag>``)