- recipe dipcall
Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies.
- Homepage:
- License:
MIT
- Recipe:
- Links:
Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies. It was originally developed for constructing the syndip benchmark dataset and has been applied to other phased assemblies, too. Dipcall can call small variants and long INDELs as long as they are contained in minimap2 alignment.
- package dipcall¶
- Versions:
0.3-0,0.2-2,0.2-1,0.2-0- Depends:
on bedtk
on htsbox
on k8
on make
on minimap2
on perl
*on samtools
on unimap
on winnowmap
- 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 dipcall
to add into an existing workspace instead, run:
pixi add dipcall
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 dipcall
Alternatively, to install into a new environment, run:
conda create -n envname dipcall
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/dipcall:<tag>
(see dipcall/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/dipcall/README.html)
