Add support for structural variants

gmc-norr / scout-annotation

Snakemake workflow for annotating VCF files

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Add support for structural variants #8

Open maehler opened 1 year ago

maehler commented 1 year ago

It should be possible to supply a VCF file of structural variants for each sample. If nothing is given, the workflow should behave as it is at the moment, otherwise the structural variants should be annotated and added to the Scout load config.

How can the files be annotated?
What annotations does Scout need?
Does genmod handle structural variants differently from SNVs?

maehler commented 1 year ago

Stumbled upon a tool that could be useful: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-05008-y