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
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
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’.