The Fixed Ploidy Variant caller: Models and methods

This section describes the model, method and estimation procedure behind the Fixed Ploidy Variant caller. The Fixed Ploidy Variant caller is designed for detecting variants in samples for which the ploidy is known. As the Fixed Ploidy Variant caller assumes, and hence can exploit, information about underlying possible allele type sites, this variant caller has particularly high specificity for samples for which the ploidy assumption is valid.