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.
As the currently implementation of excluding regions for delly may be to strict excluded regions are now handled differently.
Excluded regions can now be defined in the config-file setting exclude_regions in the calling/delly section.
In case the option is not set a predefined template file will be downloaded from https://github.com/dellytools/delly/tree/main/excludeTemplates if existing for the definied species and build.
If neither a custom region file is set nor a predefined template exists delly will be called without excluding regions.
As the currently implementation of excluding regions for delly may be to strict excluded regions are now handled differently.
Excluded regions can now be defined in the config-file setting
exclude_regionsin thecalling/dellysection. In case the option is not set a predefined template file will be downloaded fromhttps://github.com/dellytools/delly/tree/main/excludeTemplatesif existing for the definied species and build. If neither a custom region file is set nor a predefined template exists delly will be called without excluding regions.