recipe vcf2maf

Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms.

Homepage:

https://github.com/mskcc/vcf2maf

License:

APACHE / Apache-2.0

Recipe:

/vcf2maf/meta.yaml

Links:

doi: 10.5281/zenodo.593251

package vcf2maf

(downloads) docker_vcf2maf

versions:
1.6.22-0,  1.6.21-0,  1.6.20-1,  1.6.20-0,  1.6.19-1,  1.6.19-0,  1.6.18-2,  1.6.18-1,  1.6.18-0, 

1.6.22-0,  1.6.21-0,  1.6.20-1,  1.6.20-0,  1.6.19-1,  1.6.19-0,  1.6.18-2,  1.6.18-1,  1.6.18-0,  1.6.17-2,  1.6.17-1,  1.6.17-0,  1.6.16-4,  1.6.16-3,  1.6.16-0,  1.6.15-1,  1.6.15-0,  1.6.14-0,  1.6.12-0,  1.6.8-0

depends htslib:

depends perl:

depends samtools:

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 vcf2maf

and update with::

   mamba update vcf2maf

To create a new environment, run:

mamba create --name myenvname vcf2maf

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/vcf2maf:<tag>

(see `vcf2maf/tags`_ for valid values for ``<tag>``)

Notes

This package installs only vcf2maf and does not integrate with the variant-effect-predictor (VEP). To do so, please follow the instructions at https://github.com/mskcc/vcf2maf/blob/master/README.md.

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