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umccr / umccrise

:snake: DRAGEN Tumor/Normal workflow post-processing
https://umccr.github.io/umccrise/
MIT License
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MutationalPatterns: handle dbs context error #59

Closed pdiakumis closed 3 years ago

pdiakumis commented 3 years ago

Hitting this error when running on both COLO829 tumors:

There are some REF or ALT bases, that do not belong to any of the categories.
Did you forget to use 'get_dbs_context()'?

https://github.com/UMCUGenetics/MutationalPatterns/blob/440e1fe2a1a2d90057ed26ebf92a1c35c34885e7/R/count_dbs_contexts.R#L106

Think it might be originating from the upstream .get_mut_type recursive function. Will open an issue on the MutationalPatterns repo.

pdiakumis commented 3 years ago

Issue reported at https://github.com/UMCUGenetics/MutationalPatterns/issues/56