I searched the support site for references to WGS, and "whole genome sequencing", and nothing came back. One experimental data package called cgdv17 is available that includes excerpts from Complete Genomics public release. This package was apparently made back in 2011. It defines a "raggedVariant" class to handle in a unified way information from VCFs that have variants that are not shared between samples. Since then, VRanges has become available, and seems quite relevant.
Before I work on upgrading cgdv17 to use more current infrastructure such as GenomicFiles, I wanted to check with the community to see if there are approaches to working with WGS data in Bioconductor of which I am unaware.