UCSC Data Integrator and Variant Annotation Integrator

Angie S Hinrichs, Brian J Raney, Matthew L Speir, Brooke Rhead, Jonathan Casper, Donna Karolchik, Robert M Kuhn, Kate R Rosenbloom, Ann S Zweig, David Haussler, W James Kent

Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP (Liu et al., 2015) for missense mutations, ENCODE regulatory summary tracks (The ENCODE Project Consortium, 2012), and conservation scores (Siepel et al., 2005; Pollard et al., 2010). The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/. The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license. [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.