This workflow takes a VCF file and adds Variant Effect Predictor annotations using particular settings for the GDC harmonization process.
- Tested on cwltool version
1.0.20180306163216 - See GDC Reference Files
- Plugins and Dockerfile available at https://github.com/NCI-GDC/vep-tool
- Currently, we are using VEP v84 with our customized cache file (see VEP-SETUP.md for more information) or v102.