recipe mity

Mity is a bioinformatic analysis pipeline designed to call mitochondrial SNV and INDEL variants from Whole Genome Sequencing (WGS) data.

Homepage:

https://github.com/KCCG/mity

License:

MIT / MIT

Recipe:

/mity/meta.yaml

*Mity* can:

- identify very low-heteroplasmy variants, even <1% heteroplasmy when there is sufficient read-depth (eg >1000x) - filter out common artefacts that arise from high-depth sequencing - easily integrate with existing nuclear DNA analysis pipelines (mity merge) - provide an annotated report, designed for clinicians and researchers to interrogate

package mity

versions:

1.1.0-0

depends freebayes:

>=1.2

depends gsort:

>=0.1.4

depends numpy:

depends pandas:

depends pysam:

depends python:

>=3.10

depends pyyaml:

depends scipy:

depends vcfanno:

depends xlsxwriter:

requirements:

additional platforms:

Installation

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 mity

and update with::

   mamba update mity

To create a new environment, run:

mamba create --name myenvname mity

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 quay.io/biocontainers/mity:<tag>

(see `mity/tags`_ for valid values for ``<tag>``)

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