A BED or a VCF file that defines regions in the gene that typically contain variants. Specifying a hotspots file to use in a run enables the Torrent Variant Caller module to identify if a specific variant is present or absent. A hotspots file instructs the Torrent Variant Caller module to include these positions in its output files, including evidence for a variant and the filtering thresholds that disqualified a variant candidate. A hotspots file does not affect other parts of the analysis pipeline.
If you don't specify a hotspots file, the software tells only the difference between your sequence and the reference genome.
