Using PacBio/pbsv VCF for delly force genotyping (-v)?

[bbimber]

Hello,

We have a dataset of SVs created from PacBio data using pbsv. We'd like to take those SVs and use delly to genotype a dataset of Illumina WGS samples at these specific sites. We made a sites-only VCF from the PacBio data and provided this VCF as "-v" for delly call. This command dies with the error "Delly genotyping requires local SV assembly (INFO/CONSENSUS) and breakpoint (INFO/CONSBP) introduced in delly v1.1.7!", which maps to this code:

delly/src/modvcf.h

Line 291 in 3048789

std::cerr << "Error: Delly genotyping requires local SV assembly (INFO/CONSENSUS) and breakpoint (INFO/CONSBP) introduced in delly v1.1.7!" << std::endl;

I assume the problem is that the VCF lack from INFO annotations delly expects.

My question is: is there a way to use a VCF generated by another caller (pbsv in particular) as the whitelist of delly's forced genotyping?

Thanks for any help.