recipe vcf-reformatter

Fast VCF file parser and reformatter with VEP and SnpEff annotation support

Homepage:

https://github.com/flalom/vcf-reformatter

Documentation:

https://github.com/flalom/vcf-reformatter/blob/main/README.md

License:

MIT / MIT

Recipe:

/vcf-reformatter/meta.yaml

A Rust command-line tool for parsing and reformatting VCF (Variant Call Format) files, with support for VEP (Variant Effect Predictor) and SnpEff annotations. This tool flattens complex VCF files into tab-separated values (TSV) format for easier downstream analysis.

package vcf-reformatter

(downloads) docker_vcf-reformatter

versions:

0.3.0-0,  0.2.0-0

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 vcf-reformatter

and update with::

   mamba update vcf-reformatter

To create a new environment, run:

mamba create --name myenvname vcf-reformatter

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/vcf-reformatter:<tag>

(see `vcf-reformatter/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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