recipe vcf2maf-umccr

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

Homepage:

https://github.com/umccr/vcf2maf/

License:

Apache / Apache-2.0

Recipe:

/vcf2maf-umccr/meta.yaml

package vcf2maf-umccr

(downloads) docker_vcf2maf-umccr

versions:

1.6.21.20230511-0

depends htslib:

depends perl:

depends samtools:

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 vcf2maf-umccr

and update with::

   mamba update vcf2maf-umccr

To create a new environment, run:

mamba create --name myenvname vcf2maf-umccr

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-umccr:<tag>

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

Notes

This package incorporates the latest changes of the original tool [vcf2maf](https://github.com/mskcc/vcf2maf) from its main branch but released from the [umccr fork](https://github.com/umccr/vcf2maf/).

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