Target regions and hotspots files

Target regions and hotspots Browser Extensible Data (BED) files supply chromosome positions or regions as reference information during the analysis of a sequencing run. These BED files, when applied to a reference sequence in a Planned Run, or in a variantCaller plugin configuration, perform two functions:

• Target regions files narrow the analysis to your regions of interest, for example, regions that are amplified with primer panels in targeted sequencing. When a target regions file is selected in a Planned Run, the complete Torrent Suite™ Software analysis pipeline, including plugins, is restricted to the regions of the reference sequence specified in that file. Target regions files use only BED file format.

• Hotspots files instruct the variantCaller plugin to include loci known to be frequently altered in its output files, including evidence for a variant and the filtering thresholds that disqualify a variant candidate. A hotspots file affects only the variantCaller plugin, not other parts of the analysis pipeline. A hotspots file is usually a BED file, or it can be a Variant Call Format (VCF) file that is generated from a BED file by Torrent Suite™ Software during a sequencing run.

Target regions and hotspot files are listed on screens that are accessed from the Reference Sequences link. When a target regions or hotspots file is uploaded to Torrent Suite™ Software, it is assigned a specific reference sequence, and is then available for use when that reference sequence is selected during run planning.