Overview
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. 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. A hotspots file affects only the variantCaller plugin, not other parts of the analysis pipeline. (Either a BED or VCF file)
With the Torrent Browser, you add BED and VCF files to an existing reference. The reference must be listed in the Torrent Browser Admin > References tab before you can upload our BED or VCF files.
Your uploaded BED and VCF files are then available as an option when you create a new template or planned run in the Plan tab. In the template and planned run wizard, menus on the Reference chevron page offer the BED and VCF files that you uploaded to a reference.
You can optionally upload multiple BED and VCF files to a reference. In the template and planned run wizard, you specify the BED or VCF files used for each template or each run.
-
By default the variantCaller plugin calls variant candidates at hotspot positions with more sensitivity than candidates at other positions. You can customize certain variantCaller parameters separately for hotspot candidates.
-
The Torrent Browser also accepts VCF files as hotspot files.
Target regions BED files provide an option to restrict the analysis of the entire reference genome. Whole genome analysis is supported by the run type Whole Genome Analysis. Do not specify a target regions BED file on the Planning tab run registration page if the variants are to be called over the whole genome.
All regions specified in your t arget regions BED files are analyzed. Follow the instructions in Modify a BED file (before uploading your Target regions BED file) to delete lines representing regions that span variants that you do not wish to call.
The BED file coordinates (example: chr2 29443689 29443741) use zero-based indexing and a half-open interval. The start position is included, and the range extends up to, but not including, the end position.
BED files used with Ion AmpliSeq™ workflows define the internal segment only, and do not include the primer sequence.
A BED or VCF file is tied to specific reference. The coordinates within a BED or VCF file must match coordinates and the coordinate sorting in the reference genome. Torrent Suite™ Software reference genomes are sorted alpha-numerically (not by a chromosome sort). The BED files and VCF files that you use with Torrent Suite™ references must also use an alpha-numeric sort. If you upload your own reference genome, the BED and VCF files that you use with that reference must be sorted by the same method as your reference file.