update jenny's file

[jharenza]

• add histologies v21
• add tel gene alterations

Purpose/implementation Section

What scientific question is your analysis addressing?

update jenny's file merge after #6

What was your approach?

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?

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]

@runjin326 I updated this with jenny's new file, but there are two issues here:

1. DNA and RNA BS_id matchs did not consider parent_aliquot_id, so please match on those prefixes and remove the non-matching
2. we need to use independent specimens here for DNA sample_id - we can either do a sampling or use independent specimens in OpenPBTA if there is a file that spanstumor_descriptor`

Can you work on those two things? Thanks!

[runjin326]

@jharenza , so do you want me to work on this after the PR is merged? Or just directly commit on the PR?

[jharenza]

You can directly commit bc this is upstream of the rest

[jharenza]

should we go ahead and swap those in the input file?

Yes please. I think this happened before we had those longer parental aliquot IDs to match with, so all dna and rna were matched.