recipe piawka

The powerful AWK script to calculate population statistics in VCF files with support for varying ploidy and missing data

Homepage:

https://github.com/novikovalab/piawka

Documentation:

https://github.com/novikovalab/piawka/wiki

License:

MIT / MIT

Recipe:

/piawka/meta.yaml

The powerful awk script to calculate π, Dxy (or πxy, or Nei's D) and some more simple stats (Fst, Tajima's D, Ronfort's rho) in VCF files in the command line. Developed to analyze arbitrary-ploidy groups with substantial amounts of missing data. Largely inspired by https://github.com/ksamuk/pixy

package piawka

(downloads) docker_piawka

versions:

0.8.2-0,  0.8.1-0,  0.7.10-0

depends bash:

depends gawk:

>=5.0.0

depends tabix:

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 piawka

and update with::

   mamba update piawka

To create a new environment, run:

mamba create --name myenvname piawka

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/piawka:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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