The variantCaller plugin calls single-nucleotide polymorphisms (SNPs), multi-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 pre-set 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 on both manual launches of the plugin and in automatic launches through a Planned Run.