variantCaller plugin operates on input BAM files generated using Torrent Suite™ Software and requires the presence of flow signal specific tags in the BAM file.

You optionally also supply the variantCaller plugin with target regions files and hotspot files:

• Target regions files — Sequencing is restricted to specified chromosome regions that appear in the regions of interest file.

• Hotspot files — the variantCaller plugin evaluates each listed position on the genome, and reports the filtering metrics for each position, including positions that are not called as a variant. When a hotspot position receives a NOCALL rather than a reference call or a variant call, the filtering reasons in the VCF output file explain the reasons for the NOCALL.

In the 4.x and 3.6.x releases, a hotspots file can be either BED format or VCF 4.1 format. The BED format might be deprecated in a future release. Both hotspots files and targeted regions of interest files are uploaded in the Torrent Browser References page and are associated with a specific reference.