Schematic workflow. FunSeq2 consists of two components: creation of data context and variant prioritization. We processed large-scale genomics (such as 1000 Genomes and ENCODE data) and cancer resources to create the small-scale informative data context, as shown within the dashed rectangle. The variant prioritization pipeline will take user-input cancer variants and then annotate and score them against the data context. All features are used to annotate variants (shown in Additional file 1: Table S2), whereas a fraction of them are used to score variants (Additional file 1: Table S3) with the weighted scoring scheme. `Process’ contains scripts to analyze data, which can be downloaded from our website. Green arrows show the input and output of the prioritization pipeline (matched with Figure 2).