To assist researchers in annotating and prioritizing thousands of variant calls from sequencing projects, we have developed a new software tool, the Variant Annotation Integrator (VAI). Given a set of variants uploaded as a custom track in either Personal Genome SNP (pgSnp) or VCF format, the VAI returns the predicted functional effect (e.g., synonymous, missense, frameshift, intronic) for each variant. The VAI can also provide several other types of relevant information, such as the dbSNP identifier if the variant is found in dbSNP, protein damage scores for missense variants from the Database of Non-synonymous Functional Predictions (dbNSFP) (31) and conservation scores computed from multiple-species alignments. Filters are available to focus results on the variants of greatest interest. The VAI can be accessed from the Genome Browser ‘Tools’ menu or through the VAI button on the ‘Manage Custom Tracks’ page that displays after a custom track is loaded into the Browser. For more information about the VAI, see http://genome.ucsc.edu/cgi-bin/hgVai.
