Guidelines for using target regions and hotspots files

Target regions BED files provide an option to restrict analysis to regions of interest. Do not specify a target regions BED file in the Plan step of the Planned Run workflow if you want variant analysis to span an entire genome. Use the whole-genome application with a reference sequence to support whole‑genome analysis.

All regions that are included in the target regions BED file that you select are analyzed. Before you upload your target regions BED file, follow the instructions in Modify a BED file to delete lines representing regions containing variants that you do not want to call.

The BED file coordinates (for 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 that are used with Ion AmpliSeq™ panels define only the internal segment, and do not include the primer sequence.

A BED or VCF file is tied to a specific reference sequence. The coordinates in a BED or VCF file must match coordinates and the coordinate sorting in the reference sequence. Torrent Suite™ Software reference sequences are sorted alpha-numerically (not by a chromosome sort). The BED files and VCF files that you use with references must also use an alpha-numeric sort. If you upload your own reference genome sequence, the BED and VCF files that you use with that reference must be sorted by the same method as your reference file.

The variantCaller plugin calls variant candidates at hotspot positions with higher sensitivity than candidates at other positions. You can customize specific variantCaller parameters separately for hotspot candidates.

Torrent Suite™ Software accepts VCF files as hotspots files, but the VCF file must be generated by the variantCaller plugin from a hotspots BED file.

Target regions and hotspots files for use with Ion AmpliSeq™ panels can be downloaded with panel files from AmpliSeq.com.

If you need Oncomine™ panel target regions and hotspots files, contact your local Field Service Engineer.