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snakemake-workflows / dna-seq-varlociraptor

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.
MIT License
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feat: Improved handling of custom annotation fields #221

Closed FelixMoelder closed 1 year ago

FelixMoelder commented 1 year ago

This PR introduces enhanced handling of annotation fields for vembrane tables. In its previous implementation it was only possible to define a annotation field column by its name. While this is still possible it is now also allowed to define entrys by a custom name and corresponding python expression which will be passed to the vembrane table call. This allows more appealing header names in the final datavzrd report but also to retrieve only certain information from a annotation field as some are customized by vembrane for improved filtering e.g. exons and exon positions.

Apart from that, the allele frequency columns are moved to the front of the final tables as they provide helpful initial insights and users currently need to scroll to the right on most displays.

FelixMoelder commented 1 year ago

Added basic support for varlociraptor 7.0. Plots get drawn as in previous versions. Reference or alternate alleles are not considered, yet.