A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
Candidate variants are currently called based on covered and, if provided, the intersection of target regions.
To reduce runtime close regions are getting merged.
As a consequence called variants can originate from off-target regions.
These are now getting eliminated by filtering the candidate calls by target regions if provided.
Candidate variants are currently called based on covered and, if provided, the intersection of target regions. To reduce runtime close regions are getting merged. As a consequence called variants can originate from off-target regions. These are now getting eliminated by filtering the candidate calls by target regions if provided.