recipe vardict

A sensitive variant caller for both single and paired sample variant calling

Homepage:

https://github.com/AstraZeneca-NGS/VarDict

License:

MIT / MIT

Recipe:

/vardict/meta.yaml

package vardict

(downloads) docker_vardict

versions:
2019.06.04-0,  2018.10.18-1,  2018.10.18-0,  2018.09.21-0,  2018.07.25-0,  2018.07.24-0,  2018.06.21-0,  2018.04.27-1,  2018.04.27-0, 

2019.06.04-0,  2018.10.18-1,  2018.10.18-0,  2018.09.21-0,  2018.07.25-0,  2018.07.24-0,  2018.06.21-0,  2018.04.27-1,  2018.04.27-0,  2017.11.23-0,  2017.09.24-0,  2017.04.18-0,  2017.02.16-0,  2017.02.10-0,  2017.02.01-0,  2017.01.27-0,  2016.12.02-0,  2016.02.19-0,  2016.01.27-0,  2015.10.30-0,  1.8.2-2,  1.8.2-1,  1.8.2-0,  1.8.1-0

depends perl:

>=5.26.2,<5.26.3.0a0

depends vardict-java:

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 vardict

and update with::

   mamba update vardict

To create a new environment, run:

mamba create --name myenvname vardict

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/vardict:<tag>

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

Download stats

Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/vardict/README.html)