recipe biopet-vcffilter

This tool enables a user to filter VCF files.

Homepage

https://github.com/biopet/vcffilter

License

MIT

Recipe

/biopet-vcffilter/meta.yaml

This tool enables a user to filter VCF files. For example on sample depth and/or total depth. It can also be used to filter out the reference calls and/or minimum number of sample passes. There is a wide set of options which one can use to change the filter settings.

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

package biopet-vcffilter

Versions

0.2-0

Depends

• openjdk >=8,<9

• python

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install biopet-vcffilter

and update with:

conda update biopet-vcffilter

or use the docker container:

docker pull quay.io/biocontainers/biopet-vcffilter:<tag>

(see biopet-vcffilter/tags for valid values for <tag>)

Notes

biopet-vcffilter 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-vcffilter’. 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-vcffilter -Xms512m -Xmx1g’.

Link to this page

Render an 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-vcffilter/README.html)