PennCNV – Implements a hidden Markov model that integrates multiple sources of information to infer CNV calls for individual genotpes samples, widely-used.
Biofilter, Biobin – Provides methods for prioritizing and analyzing variants singly or in groups.
PLATO, ATHENA – Provides platforms for QC and integrating multiple methods of analysis.
Synthesis-View, PheWAS-View and Phenogram provides visualization tools for genome and phenome-wide data=. These tools are also offered via a web interface at http://visualization.ritchielab.psu.edu/.