Create list of cancer group/path dx discrepancies based on high-confidence methyl subtypes

[jharenza]

What data file(s) does this issue pertain to?

histologies.tsv

What release are you using?

v12

Put your question or report your issue here.

Create a list of samples whose pathology diagnosis and/or finalized molecular subtype & cancer group do not agree with the corresponding high confidence (>= 0.8 methyl score) methylation subtype calls. This methylation subtype mapping file may be helpful.

To match methylation with tumor samples, use a match id, such as:
https://github.com/PediatricOpenTargets/OpenPedCan-analysis/blob/0b21ac4d68adeafe2930183f509f99615db4e80d/analyses/molecular-subtyping-HGG/07-HGG-molecular-subtyping-combine-table.Rmd#L63-L65

We will have these samples go through pathology checks.