About the variantCaller plugin

The variantCaller plugin calls single-nucleotide polymorphisms (SNPs), multinucleotide polymorphisms (MNPs), insertions, deletions (INDELs), and complex variants in a sample across a reference genome or within a targeted subset of that reference in Torrent Suite™ Software.

You can set the plugin to run automatically after a sequencing run is completed, or you can run the plugin manually for completed runs.

When you configure the variantCaller plugin, you can adjust parameter settings to affect the stringency of the variant calls that are made on your data. Adjustments to the parameters balance the specificity (that is, false positive calls) and sensitivity (that is, true positive calls). For more information, see variantCaller plugin configuration.

These parameter settings, when combined with the reference genome that you select, a target regions file, and a hotspots file, comprise a configuration that you can save, then use for subsequent runs of the variantCaller plugin. You can also select a predefined configuration that is included with Torrent Suite™ Software.

Preconfigured plugin settings are available as predefined or custom configurations that are available when you configure the variantCaller plugin. Use these configurations to save significant setup time. Predefined configurations for use with the Ion AmpliSeq™ and Ion AmpliSeq™ HD research applications can also be downloaded from AmpliSeq.com. For more information, see Import panel files and parameters.