- recipe biopet-vcffilter
This tool enables a user to filter VCF files.
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¶
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-vcffilter and update with:: mamba update biopet-vcffilter
To create a new environment, run:
mamba create --name myenvname biopet-vcffilter
myenvnamebeing 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-vcffilter:<tag> (see `biopet-vcffilter/tags`_ for valid values for ``<tag>``)
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'.