Generic variant calling pipeline

This pipeline is a generic re-implementation of our human-centric variant calling pipelines. It skips several of the more in-depth post-alignment metrics and allows users to provide any mapping reference they want in FASTA format.

For usage instructions, please see below.

Documentation

1. What happens in this pipeline?
2. Installation and configuration
3. Running the pipeline
4. Output
5. Troubleshooting
6. Developer guide