sv-callers workflow

sv-callers is a Snakemake-based workflow that combines several state-of-the-art tools for detecting structural variants (SVs) in whole genome sequencing data. This workflow is easy to use and to deploy on any Linux-based machine. In particular, the workflow supports automated software deployment, easy configuration and addition of new analysis tools as well as enables to scale from a single computer to different HPC clusters with minimal effort.

The workflow includes the following

SV callers

• Manta (1.1.0)
• DELLY (0.7.7)
• LUMPY (0.2.13)
• GRIDSS (1.3.4)

and post-processing tools

• BCFtools (1.9)
• SURVIVOR (1.0.6)