ABSTRACT
This chapter presents the algorithms used by Exomiser and Genomiser together with a series of practical tutorials. Exomiser and Genomiser are software suites developed by the group to enable start to finish phenotype-driven analysis of WES and WGS data. Genomiser expands the Exomiser by adding functions to analyze and prioritize non-coding variants. Both algorithms make use of many of the filtering and prioritization methods, and additionally use phenotype analysis to reorder the candidate list. PHenotypic Interpretation of Variants in Exomes (PHIVE) ranks candidate genes according to the average of variant scores and phenotypic relevance scores. The human/interaction PHIVE (hiPHIVE) method calculates phenotypic similarity not only for mouse, but also for zebrafish and human data. The Phenotypic Interpretation of eXomes (PhenIX) application was designed to evaluate the results of a clinical exome that essentially enriches exons as with exome sequencing but restricts the capture probes to genes known to have a disease association.
