Fig. 6. Comparison of RegTools with other tools for identifying cis-acting splice-associated variants.

A Conceptual diagram of contrasting approaches employed by various tools for identifying cis-acting splice-associated variants (red dots). For this example, the splice variant window (purple boxes) for RegTools is its default splice variant window employed for our main analyses. An italicized tool name indicates that the tool only considers genomic data for making its calls, instead of a combination of genomic and transcriptomic data. B Venn diagram comparing the splice-associated variants identified by RegTools, using its default splice window parameter, MiSplice, and SAVNet. C UpSet plot comparing splice-associated variants identified by RegTools using both the -E and -I splice variant window parameters to those identified by other splice variant predictors and annotators using their default settings. Each tool’s total number of variant predictions is shown on the left sidebar graph. The number of variants specific to each tool or shared between different combinations of tools is indicated by the bar graph along the top, with the individual or connected dots indicating the tools. Source data are provided as a Source Data file. ‘VEP’ refers to the Variant Effect Predictor.