LINX is designed for the analysis of cancer samples and the pipeline isn't applicable to generic disease studies. Any recommendations for general annotation, such as of germline whole genome sequencing of Parkinson's disease? I have viewed StructuralVariantAnnotation but my impression is that its aimed at variant software developers rather than data analysts.

The vast majority of germline SVs are simple, isolated events that can be analysed in a similar manner to SNVs and indels. This is definitely not the case for somatic SVs, hence why the software available for handling complex SVs is generally written with somatic variation as the primary use case.

I have viewed StructuralVariantAnnotation but my impression is that its aimed at variant software developers rather than data analysts.

SVA's primary use case is as a breakpoint-centric framework for the analysis and interpretation of genomic rearrangements. Yes, it does help immensely in developing SV analysis packages but it is also useful for end-user ad-hoc analysis.

If the events you are analysing can be processed in the interval-centric GRanges notation provided by VariantAnnotation, then you can get away with a much simpler analysis. If they can't, then you need to deal with the full complexity that comes with breakpoint-based analysis. Unfortunately, the ecosystem for actually performing breakpoint-centric analysis is currently quite small. Comprehensive analysis is likely to require the development of additional R packages on top of SVA to actually perform the analysis (e.g. much like svaRetro & svaNumt).