- recipe vcf2maf-umccr
Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms
- Homepage:
- License:
Apache / Apache-2.0
- Recipe:
- package vcf2maf-umccr¶
- Versions:
1.6.21.20230511-0- Depends:
on htslib
on perl
on samtools
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install vcf2maf-umccr
to add into an existing workspace instead, run:
pixi add vcf2maf-umccr
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install vcf2maf-umccr
Alternatively, to install into a new environment, run:
conda create -n envname vcf2maf-umccr
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/vcf2maf-umccr:<tag>
(see vcf2maf-umccr/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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/).
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/vcf2maf-umccr/README.html)
