recipe tb_variant_filter

VCF variant filter optimised for filter M. tuberculosis H37Rv variants

Homepage:

http://github.com/COMBAT-TB/tb_variant_filter

License:

GPL / GPL-3.0

Recipe:

/tb_variant_filter/meta.yaml

tb_variant_filter filters variants in VCF filters, with a focus on the kinds of filtering done with variants found relative to M. tuberculosis H37Rv

package tb_variant_filter

versions:

0.4.0-0,  0.3.6-0,  0.3.5-0,  0.3.0-0,  0.2.0-1,  0.2.0-0,  0.1.3-0,  0.1.2-0,  0.1.1-0, 

0.4.0-0,  0.3.6-0,  0.3.5-0,  0.3.0-0,  0.2.0-1,  0.2.0-0,  0.1.3-0,  0.1.2-0,  0.1.1-0,  0.1.0-0,  0.0.1-0

depends intervaltree:

depends lxml:

depends neo4j-python-driver:

depends pandas:

depends python:

>=3.7

depends requests:

depends vcfpy:

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 tb_variant_filter

and update with::

   mamba update tb_variant_filter

To create a new environment, run:

mamba create --name myenvname tb_variant_filter

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/tb_variant_filter:<tag>

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

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Link to this page

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