recipe mutserve

Mutserve2 is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data.

Homepage:

https://github.com/seppinho/mutserve

License:

MIT

Recipe:

/mutserve/meta.yaml

Mutserve Variant Calling: ``` mutserve call

--reference rCRS.fasta --output HG00096.vcf.gz --threads 4 *.bam

``` The full list of parameters is available [here](https://github.com/seppinho/mutserve#:~:text=output%20AnnotatedVariants.txt-,Parameters,-Parameter).

Mutserve Variant Annotation: ``` mutserve annotate

--input variantfile.txt --annotation rCRS_annotation_2020-08-20.txt --output AnnotatedVariants.txt

``` `rCRS.fasta`, `rCRS_annotation_2020-08-20.txt`, and `rCRS_annotation_descriptions.md` are available in the Mutserve2 repository (`$MUTSERVE_DATA/`).

package mutserve

(downloads) docker_mutserve

versions:

2.0.3-0

depends openjdk:

>=11

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 mutserve

and update with::

   mamba update mutserve

To create a new environment, run:

mamba create --name myenvname mutserve

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/mutserve:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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