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.
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fix: fusion candidate filtering and add HGVSc to variant datavzrd report #299
The fusion calling workflow fails in case of candidate calls being filtered.
This happens as vembrane filter does not keep entries coordinate sorted but groups records by fusion mates.
Therefore varlociraptor preprocess fails as it expects coordinate sorted input.
Further a minor change to the variant calling datavzrd report has been made.
The report now shows HGVSc instead of HGVSg values. HGVSg values are still used for Genome Nexus linkouts but the entry itself is now hidden.
The fusion calling workflow fails in case of candidate calls being filtered. This happens as
vembrane filterdoes not keep entries coordinate sorted but groups records by fusion mates. Thereforevarlociraptor preprocessfails as it expects coordinate sorted input.Further a minor change to the variant calling datavzrd report has been made. The report now shows HGVSc instead of HGVSg values. HGVSg values are still used for Genome Nexus linkouts but the entry itself is now hidden.