v12 hgg subtyping (10/N)

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update HGG subtyping for v12 data release.

What was your approach?

• update all outmoded gene symbols
• update most of the 10 module scripts
• update logic for IHG subtyping to include methylation
• updated HGG/DMG/IDH to include methylation
• regenerated new results with v12 pre-release datasets
• updated README

What GitHub issue does your pull request address?

• Updated analysis: HGG subtyping to include GENCODE v39 gene symbols ticket-tracker-OPC#487

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

Which areas should receive a particularly close look?

• Review all updated module scripts to check if the logic makes sense. Specifically, the subtyping script 07 is revamped to include methylation classification in the HGG subtyping.
• compare with the previous updated IHG subtyping and which was very confusing.
• Review the subtyping results

Is there anything that you want to discuss further?

Observed 5 DMG, H3 K28 samples that can be subtyped as IHG, ROS1-altered. Seems not mutually exclusive.

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

YES

Results

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

v12 HGG subtyping results

What is your summary of the results?

v12 HGG subtyping 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]

I think I got all of the logic updated here, but now trying to remedy some missing files in the final output tables created in script 07, but calling it quits for tonight.

• Many targeted panel RNA fusion are missing due to this comment - missing in fusion summary
• A handful of DNA are missing - I think due to missing in MAF: "BS_DBH8YWA1" "BS_EE73VE7V" "BS_XNYQS1WG" "BS_XQF18WZP"
• Some RNA-Seq missing, have to check this still
• A handful of methyl missing, have to check this as well