Fig. 2
Example of the Integrative Genomics Viewer Navigator (IGVNav) interface, associated features, and input/output files. a IGVNav is a simple plugin for IGV that provides a separate application window for recording results of manual review. The 1-Base? button can be selected for 1-base input files (default is 0-base). The “S” button will sort the read sequences in the data tracks so that mismatches appear at the top. The navigation bar displays variant information and allows for movement between variants. The Call, Tags, and Notes sections allow manual reviewers to annotate variants (Table 1), which is reflected in the output file. The Save button is used to update the output file. b An IGVNav input file consists of a header line and data for the first five columns (chromosome [chr], start coordinate [start], stop coordinate [stop], reference allele [ref], and variant allele [var]). Each line represents a variant that will be individually visualized using IGV. c During manual review, the input file is updated by clicking on the Save button. This will print the call, tags, and notes associated with individual variants to the original input file.
