variantCaller plugin advanced parameters

Advanced parameter settings for the variantCaller plugin allow additional customization of the variant calling algorithm and are for use only by advanced users.

In general, you can safely customize parameters for SNP calling. For INDEL calling, changes to the parameters tend to have a significant impact on the number of INDELs called. As a result, consider the tradeoff between sensitivity and specificity for INDEL calls when you optimize customized parameters.

The variant calling pipeline in the variantCaller plugin contains three modules:

• Torrent Variant Caller module—The Torrent Variant Caller module evaluates the list of candidates and examines evidence for the variants in flow space.

• FreeBayes module—The FreeBayes module, as a candidate generator, generates lists of variant candidates.

• Long INDEL Assembler module—Some long INDELs, if improperly aligned to the reference genome, may not be discovered and evaluated by the FreeBayes and the Torrent Variant Caller modules. The purpose of the Long INDEL Assembler module is to call these long INDELs. A unification step in the pipeline combines the variants that are called by the Torrent Variant Caller and the Long INDEL Assembler module into one VCF file. The VCF file is available to the software.