variantCaller plugin

The variantCaller plugin calls single-nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs), insertions, deletions, and block substitutions in a sample across a reference or within a targeted subset of that reference.

This plugin provides optimized preset parameters for many experiment types. It can also be customized. After you find a parameter combination that works well on your data and that has the balance of specificity and sensitivity that you want, you can save that parameter set and reuse it in your research. Customization is supported when you run the plugin after a sequencing run and when the plugin is run through a Planned Run.

For details about the variantCaller plugin, see Variant calls in Torrent Suite Software.