snakemake-workflows / dna-seq-mtb

A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
MIT License
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feat: Add event for splice mutations, consider FFPE substrates #1

Closed FelixMoelder closed 2 years ago

FelixMoelder commented 2 years ago

This PR introduces an additional event for splice mutations. Further, samples being ffpe substrates can now be defined in the sample sheet. This information will be considered when rendering the scenario. Additionally, the mutational_burden_events column has been removed from the sample sheet. These events will be set automatically for tumor and normal samples, now. At last, additional test cases where added for the following scenarios: