References Management Guide

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Torrent Suite Software space on Ion Community

References Management Guide TOC

Target Regions Files and Hotspot Files

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 t arget regions files and hotspot files on your system, click the admin gear menu References option:

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

The left navigation tabs open Hotspots 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. See 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). See Manage Target Regions Files and Hotspot Files for more information.

Details page

File details and download

In either the Hotspots or Target Regions page, when you click on a hotspot file name or a target regions file name, a details page opens with details of both the hotspot file and the related target regions file (provided both are available):

In these details sections, you can do the following:

• Click on the Processed File link to download the hotspot or target regions file.
• Add a description or notes.
• Uncheck the Enable check box to prevent the file from being used in an analysis.

Click the Save Change button to save your description, notes, or Enable status.

Zip file details and download

For files imported for ampliseq.com, the details page also shows the zip file that was imported from ampliseq.com:

Upload log file

The details page also has a section with the validation log from when the hotspot and target regions files were originally uploaded.

BED file formats and examples

See BED File Formats and Examples .

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