fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.
Releases of fgbio are available from the GitHub Releases page for the project. Start by downloading the
.jar file for the latest release.
To run fgbio you will need Java 8 (aka Java 1.8) or later installed. To see the version of Java currently installed run the following in a terminal:
If the reported version on the first line starts with
1.8 or higher, you are all set.
Once you have Java installed and a release downloaded you can run:
java -jar fgbio-2.0.2.jarto get a list of available tools
java -jar fgbio-2.0.2.jar <Tool Name>to see detailed usage instructions on any tool
When running tools we recommend the following set of Java options as a starting point though individual tools may need more or less memory depending on the input data:
java -Xmx4g -XX:+AggressiveOpts -XX:+AggressiveHeap -jar fgbio.jar ...
To save typing this every time you may wish to setup a shell alias, for example:
alias fgbio="java -Xmx4g -XX:+AggressiveOpts -XX:+AggressiveHeap -jar /path/to/fgbio.jar
Each tool has detailed uage and argument documentation that can be viewed at the command line by running the tool in question with no arguments.
Documentation is also available online:
The primary mechanism for getting help is to log an issue on the project’s GitHub Issues page.
If requesting help with a tool that is failing or producing undesirable results, please include:
fgbio is open source software released under the MIT License.