SnpEff is integrated with other tools commonly used in sequencing data analysis pipelines.

Most notably [Galaxy](http://galaxyproject.org/) and Broad Institute's Genome Analysis Toolkit ([GATK](http://www.broadinstitute.org/gatk/) projects support SnpEff.
By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.

More details about integration [here](se_integration.md#integration-gatk-and-galaxy).

This is a screen capture from a Galaxy server (click to enlarge):
[![](images/snpEff_galaxy_small.png)](images/snpEff_galaxy.png){: .center}
