recipe vafator

VAFator annotates the variants in a VCF file with technical annotations extracted from one or more BAM alignment files. We implement a set of basic coverage annotations and also more sophisticated published annotations used to assess the quality of every variant call.

Homepage:

https://github.com/tron-bioinformatics/vafator

License:

MIT / MIT

Recipe:

/vafator/meta.yaml

Links:

doi: 10.5281/zenodo.6976425

package vafator

versions:

2.2.0-0,  2.1.0-0,  2.0.3-0,  2.0.2-0,  2.0.1-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.6-0, 

2.2.0-0,  2.1.0-0,  2.0.3-0,  2.0.2-0,  2.0.1-0,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.6-0,  1.2.5-0,  1.2.4-0,  1.1.4-0,  1.1.2-0,  1.1.0-0,  0.4.0-0,  0.3.4-0,  0.3.3-0

depends cyvcf2:

>=0.30.14,<0.31

depends logzero:

>=1.7.0,<1.8

depends pandas:

>=1.3.3,<1.4

depends pybedtools:

>=0.9.0,<0.10

depends pysam:

>=0.19.1,<0.20

depends python:

>=3.7,<=3.9

depends scipy:

>=1.8.1,<1.9

requirements:

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 vafator

and update with::

   mamba update vafator

To create a new environment, run:

mamba create --name myenvname vafator

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/vafator:<tag>

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

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