The Fixed Ploidy Variant Detection tool: Models and methods
This section describes the model, method and estimation procedure behind the Fixed Ploidy Variant Detection tool. The Fixed Ploidy Variant Detection tool is designed for detecting variants in samples for which the ploidy is known. As the Fixed Ploidy Variant Detection tool 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.
Subsections
- The Fixed Ploidy Variant Detection tool
- The model for the Fixed Ploidy Variant Detection tool
- Deriving the posterior probabilities of the site types
- Estimating the parameters in the model for the Fixed Ploidy Variant Detection tool
- Updating equations for the prior site type probabilities
- Updating equations for the error rates