hotspots file

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 Torrent Variant Caller to identify if a specific variant is present or absent. A hotspot file instructs the Torrent Variant Caller to include these positions in its output files, including evidence for a variant and the filtering thresholds that disqualified a variant candidate. A hotspot file affects only the variantCaller plugin, not 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.