recipe dipcall

Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies.

Homepage:

https://github.com/lh3/dipcall

License:

MIT

Recipe:

/dipcall/meta.yaml

Links:

doi: 10.1038/s41592-018-0054-7

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

(downloads) docker_dipcall

versions:

0.3-0,  0.2-2,  0.2-1,  0.2-0

depends bedtk:

depends htsbox:

depends k8:

depends make:

depends minimap2:

depends perl:

*

depends samtools:

depends unimap:

depends winnowmap:

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 dipcall

and update with::

   mamba update dipcall

To create a new environment, run:

mamba create --name myenvname dipcall

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/dipcall:<tag>

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

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Link to this page

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