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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: fusion calling #222

Closed FelixMoelder closed 4 months ago

FelixMoelder commented 1 year ago

These changes introduce fusion calling in addition the variant calling. There for arriba is applied for calling variants. As vep does not provide any helpful information it is skipped for fusion calls. Instead annotation is performed by additional scripts that come with the arriba package. To define a what kind of analysis shall be performed for a sample an additional column named datatype has been added to the samplesheet allowing either rna or dna. As file name extensions within the pipeline are separated into variants and fusions we probably should unify this as the former one might also be too generic. For fusion calls a separte datavzrd report will be created adding a new category showing up in the final snakemake report.

FelixMoelder commented 10 months ago

To get this running we need https://github.com/suhrig/arriba/pull/191 being merged and a new release of arriba.