Browser Extensible Data (BED) files and Variant Call Format (VCF) files supply chromosome positions or regions. When applied to a reference genome in the Torrent Browser, these files perform these two functions:

• Targeted regions of interest Specifies your regions of interest, for instance the amplified regions that are used with targeted sequencing. Analysis in the complete Torrent Suite™ Software analysis pipeline, including plugins, is restricted to only the specified regions. (BED file only)

• Hotspot Instructs the Variant Caller to include these positions in its output files, including evidence for a variant and the filtering thresholds that disqualified a variant candidate. Only affects the variantCaller plugin, not other parts of the analysis pipeline. (Either a BED or VCF file)

Target regions files and hotspot files are listed in the admin References tab. These files are uploaded to a specific reference and available for use only when that reference is used for an analysis.

To view the target regions files and hotspot files on your system, click Settings () > References:

In the References tab left navigation panel, click the Target Regions or Hotspots tab:

The left navigation tabs openHotspots or Target Regions pages, which are very similar:

Both Hotspots and Target Regions pages offer the following actions:

• Click the file name to open its details page.

• Use the references selection menu (default Show all References) to display only files of one reference.

• Click the Add Hotspot or Add Target Regions button to upload a new file (to associate with any reference).