Genotyping structural variation in variation graphs with the vg toolkit
This repositiory contains the commands and scripts used for Genotyping structural variation in variation graphs with the vg toolkit, 2019, in press. They are primarily dependent on toil-vg, which can run most other dependencies via Docker. Github issues is the best place to raise questions or concerns.
Whole genome experiments
These were run on AWS via Toil. In theory, they could use any other framework that Toil supports, though the scripts will have to be modified accordingly.