The Track Manager tool in NextGENe allows for import of variant annotation from external databases that can be automatically queried for use in both the mutation report (figure 1) and the variant comparison report. Tracks such as dbSNP, COSMIC, 1000 genomes, dbNSFP, and NHLBI GO Exome Sequencing Project (ESP) can be added to your projects, as well as your own custom database. Once a track is imported for a given genome build, it can be automatically queried for every new project run against that genome or it can be queried manually in the NextGENe Viewer.
Figure 1: The NextGENe Mutation Report with annotation from multiple tracks.
There are four databases with specialized support. More information on some of these can be found in the ‘References' dialog of the NextGENe ‘Help' menu.