recipe biopet-vcfstats

Vcfstats is a tool that can generate metrics from a vcf file.

Homepage:

https://github.com/biopet/vcfstats

License:

MIT

Recipe:

/biopet-vcfstats/meta.yaml

Vcfstats is a tool that can generate metrics from a vcf file.

- General stats (default, can be disabled) - Genotype stats (default, can be disabled) - Sample compare (default, can be disabled) - Sample distributions (default, can be disabled) - Field histograms

This tool can run locally single threaded but also on a Apache Spark cluster.

For documentation and manuals visit our github.io page: https://biopet.github.io/vcfstats

package biopet-vcfstats

(downloads) docker_biopet-vcfstats

versions:

1.2-1,  1.2-0,  1.1-2,  1.1-1,  1.1-0,  1.0-2,  1.0-1,  1.0-0

depends openjdk:

>=8,<9

depends python:

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 biopet-vcfstats

and update with::

   mamba update biopet-vcfstats

To create a new environment, run:

mamba create --name myenvname biopet-vcfstats

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/biopet-vcfstats:<tag>

(see `biopet-vcfstats/tags`_ for valid values for ``<tag>``)

Notes

biopet-vcfstats is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-vcfstats'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-vcfstats -Xms512m -Xmx1g'.

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Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/biopet-vcfstats/README.html)