Recalculate coding TMB with updated Lancet BED file

[cansavvy]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR is updating the TMB coding calculations given the updated Lancet WXS BED file that has been added in v13.

What was your approach?

Because the SNV data itself did not changed, I re-used the latest snv database set (v11) and only recalculated the coding TMB files by revising the WXS coding BED file and then re-running only the 03-calculate-tmb.R script. Based on my knowledge of the changes, nothing else should have to be re-run.

*a minor set of changes I also slipped in in addition to the main BED file changes were some comments and filename changes where I noticed I was still mistakenly referring to exons when I actually meant cds coding sequences.

What GitHub issue does your pull request address?

#440

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

Does everything seem in order and does it follow what is expected based on #440?

Results

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

Revised results have been uploaded to S3. This includes:

• updated intersection BED files that were used
  • https://open-pbta.s3.amazonaws.com/data/snv-consensus-bed/intersect_cds_lancet_strelka_mutect_WGS.bed
  • https://open-pbta.s3.amazonaws.com/data/snv-consensus-bed/intersect_cds_lancet_WXS.bed
• updated zip file snv-consensus-20200121.zip (Note the only file of the three files within here that has changed is pbta-snv-consensus_snv_tmb_coding_only.tsv, but for consistency's sake, I uploaded the data in the same way and format that the other editions were.
  - https://open-pbta.s3.amazonaws.com/data/snv-consensus/snv-consensus-20200121.zip

What is your summary of the results?

Most of the TMB results are the same, the only thing that has been changed is the denominator for the WXS coding data. The all mutations TMB did not change because Lancet was not used for the all mutations TMB.

Reproducibility Checklist

This was done in the original PRs for this analysis.

• 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

I took a quick scan through these to make sure no comments needed to be updated in the READMEs and I believe we are set.

• 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.

[jaclyn-taroni]

👍 this implementation is consistent with my understanding of #440. Thank you for also making the exon -> cds change!