(8/N) v13 release: Run EPN subtyping for v13

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

v13 release: Run EPN subtyping for v13

What was your approach?

v13 release: Run EPN subtyping for v13

What GitHub issue does your pull request address?

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

01/03 script: Replace ID with match_id from histologies. 02 script: combined tumor-only-snv with snv

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• [ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [ ] This analysis has been added to continuous integration.

Documentation Checklist

• [ ] This analysis module has a README and it is up to date.
• [ ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [ ] The analytical code is documented and contains comments.

[jharenza]

Checking v12 vs v13, BS_M3C0MZC9 and BS_52VS6HDC are missing ZFTA subtypes.

BS_M3C0MZC9 has ZFTA--RELA in the putative oncogenic file, but is not in the fusion summary file, so the fusion summary module may need a check.

[jharenza]

@zzgeng this one is all updated - needed a lot of rework, but looks like all missing fusions are now included and more samples which were likely previously missed have subtypes now.

[jharenza]

closing due to merge issues