We're going to pretty great lengths in AnnotateCohort and AnnotateDataset to prepare SV data for Seqr. That's not relevant to Talos, and we can pull the joint-called VCFs instead
This would be an infinitely more versatile starting point for other users, SVAnnotate is a GATK-suite tool.
We could still ingest as a MT, or we could annotate directly with any of the VCF anno/parsing tools. Paging @brentp 👀
We're going to pretty great lengths in AnnotateCohort and AnnotateDataset to prepare SV data for Seqr. That's not relevant to Talos, and we can pull the joint-called VCFs instead
This would be an infinitely more versatile starting point for other users, SVAnnotate is a GATK-suite tool.
We could still ingest as a MT, or we could annotate directly with any of the VCF anno/parsing tools. Paging @brentp 👀