How to call SVs between reference genomes and force those SVs to be genotyped in WGS samples?

Question

[William]

How to best call SVs between related reference genomes and force those SVs to be genotyped in a larger set of WGS samples?

The discovered SVs and forced genotyping results should be in the co-ordinate space of a single primary reference genome (if possible. ) At least the forced genotyping results should be in a VCF file.

I have had mixed success with trying tools that claim to be able to do this.

Sometimes:

• SV discovery and genotyping in WGRS works
• SV discovery fails, for example because SV disovery only accepts BAM files, and the alignments are too long to represent in BAM (only SAM and CRAM can represent long chromosome to chromosome alignment cigar strings)
• SV discovery works, but forced genotyping fails, because the forced genotyping tool is picky about how the input SVs should be represented
• SV discovery works, but the forced genotyping result's don't make sense after manual inspection in IGV. And also not against single WGS sample SV discovery.

So I am wondering if anyone know a robust combination of bio-informatics tools for this job.