PCGR v2 support: Handle VAF_TUMOR and ACTIONABILITY_TIER

umccr / RNAsum

Pipeline for generating RNAseq-based cancer patient reports

https://umccr.github.io/RNAsum/

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PCGR v2 support: Handle VAF_TUMOR and ACTIONABILITY_TIER #169

Closed pdiakumis closed 1 month ago

pdiakumis commented 1 month ago

The AF_TUMOR and TIER columns have been renamed in PCGR v2 to VAF_TUMOR and ACTIONABILITY_TIER, respectively. The latter column's values also don't have a TIER prefix any more, so handling those in the parser itself. Tested on one sample locally and it works. Fixes #168.

ohofmann commented 1 month ago

@scwatts Would the tier re-name cause an issue with sash's rescue approach?