TCGA Consensus and Comparison Revised (1 of 2)

[cansavvy]

Purpose/implementation Section

What scientific question is your analysis addressing?

If we run the TCGA data through the same variant callers and consensus methods we used for PBTA data, do we get a comparison that more accurately meets our expectations? (aka that adults have a higher tumor mutation burden).

The next PR in this series will carry over the new dataset to the tmb-compare-tcga analysis.

What was your approach?

• Both TMB calculations for both PBTA and TCGA have been switched to only use Mutect2 and Strelka2. I had to re-run these on AWS.
• I ran the TCGA files from v14 through the same pipeline we used for the PBTA data. You will note that there were a few metadata cleaning steps that needed to be adjusted for TCGA so there is a new option (--tcga) that needs to be used for the 03-calculate-tmb.R script.
• You may note that I removed the word "Consensus" from the results files. This is because these TMB results are no longer using the official consensus maf file. Is there another file notation that would make this more clear?

What GitHub issue does your pull request address?

#257

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

Which areas should receive a particularly close look?

• The BED files for PBTA do need to be fixed see Updated analysis: bedtools creation of bed files for TMB #564 , but that will be in a different PR.
• All mentions of WGS related files in the TCGA are placeholders because there is not actually any WGS data in TCGA. I haven't made adjustments to make it so WGS options can be dropped completely. Perhaps this is a thing for the next PR?
• Is there anything where the TCGA data is not being handled properly by the snv-caller pipeline?

Results

This analysis needs to be run in AWS, and because of issues noted for the bed files for PBTA #564 I will end up re-running this in AWS. So do not be too concerned with the exact results, but more what we need to know at this stage is if the changes in the tmb calculations otherwise seem right.

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.

[cansavvy]

For now, this needs to be added in somewhere, but I think it will be in a future data release.

[jashapiro]

Looks good, but I have a couple minor questions and comments. I didn't really look at results, as we know that the bed file creation may require updating before those are final.

[jashapiro]

I just made a few changes to the split_mnv function that probably should have been in it from the start, but they affect code here. A few other little questions, one of which (probably not directly stated, is whether the union() (or union_all) call should also join by end position, as well as the other join_cols elements.

[jashapiro]

Looks good, but this time I did look at the plots, and I', not sure what is going on with analyses/snv-callers/plots/tcga-comparison/tcga-upset_median_vaf_plot.png.

It also looks like analyses/snv-callers/plots/tcga-comparison/tcga-upset_plot.png, analyses/snv-callers/plots/tcga-comparison/tcga-vaf_correlations_plot.png, analyses/snv-callers/plots/tcga-comparison/tcga-variant_classification_plot.png, and analyses/snv-callers/plots/tcga-comparison/tcga-vaf_correlations_plot.png have some errors now, in particular that the latter three are plotting the same set twice, with no lancet data.

Those changes don't seem to be related to the rest of the changes in this PR, so perhaps those files should be reverted? Or will they be updated later?

[cansavvy]

Those changes don't seem to be related to the rest of the changes in this PR, so perhaps those files should be reverted? Or will they be updated later?

Yeah, that will be in a next PR after I have the real data run from AWS. I didn't realize they were changed, I might have ran the data through as a check at some point. I'll revert remove the TCGA notebook for now and have a next PR with the "real" one.

[jashapiro]

I'll revert remove the TCGA notebook for now and have a next PR with the "real" one.

While you are at it, probably worth removing the .pngs as well.

[jashapiro]

LGTM