the variantCaller plugin provides several ways of handling its parameter options:

• You can select one of the variantCaller plugin default pre-set parameter groups. the variantCaller plugin provides these defaults that are optimized for several experiment types.

• You can start with one of the variantCaller plugin default pre-set parameter groups and then make your own customizations in the variantCaller UI.

• You can import parameter settings that are optimized for fixed panels and community panels in ampliseq.com. (Optimized parameter sets for custom designs are not supported in this release.)

• You can download the parameters used in a variantCaller run and then either customize those parameters or reuse them in future variantCaller runs.

TVC's default parameters setting groups are organized according to these attributes:

• Variant frequency Somatic settings are optimized to detect low frequency variants. Germ-line settings are optimized for high frequency settings.

• Sequencing instrument The Ion PGM™ or the Ion Proton™ sequencer. Parameter defaults are different for Ion Proton™ data than for Ion PGM™ data.

• Stringency High stringency settings are optimized to minimize false positives. Low stringency settings minimize false negatives.

• TargetSeq Two sets of defaults are optimized for TargetSeq™ data.