There is one folder for each dataset with the commands to download/prepare the data and genotype SV with vg and the other methods.
- Human Genome Structural Variation Consortium (HGSVC)
- Genome in a Bottle (GiaB)
- Pseudo-diploid CHM genome (CHMPD)
- SV catalog from Audano et al. Cell 2019 (SVPOP)
There is also a toil-scripts folder with helper scripts to were used to run the analysis on AWS.
The commands for the evaluation, using Snakemake, are available in the sveval folder.
The VCFs produced produced by vg and the other methods across these datasets are available at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=vgsv2019/vcfs/.