The UCSC Genome Browser team is pleased to announce the release of a new command-line tool for annotating variants, vai.pl. This program is similar to our web-based Variant Annotation Integrator (VAI), except it allows for bypassing the variant limit imposed by web-based VAI, and does not require connections to UCSC, allowing annotation of private clinical data.

Along with the release of this program, we have published a new blog post with some background on both web-based and command-line VAI, as well as some example usage to serve users. vai.pl is available for download from the genome-browser store, via purchase of the GBiB, GBiC, or full source, which are free for non-commercial use.

As usual, questions about this program or any other program, tools, or data at the UCSC Genome Browser should be directed to our mailing lists: genome@soe.ucsc.edu, or for private questions: genome-www@soe.ucsc.edu.

Thanks to Angie Hinrichs and Christopher Lee for the development and testing of the program.