Gigwa aims at managing genomic and genotyping data from NGS analyses. It is a tool targeted at users with little computer expertise, providing means to explore visually large amounts of genotyping data by filtering it based not only on variant features including functional annotations, but also on genotypes themselves. It also offers several popular export formats and a density chart visualizer.
Try Gigwa online with public datasets at http://gigwa.southgreen.fr/
Check the wiki:
The source code is available in this repository. It uses Maven for dependency management and requires the following dependencies to be present in your workspace :