V11 Release

[yuankunzhu]

Purpose/implementation

data release updates for v10

• changes:
  • Add putative oncogenic fusions from fusion filtering and prioritization analysis
  • Update consensus SNV/indels to contain consensus MNVs
  • Add RNA-Seq collapsed matrices - wrong files (tables of transcripts removed) were included with V10

Issue/Caveats

Directions for reviewers

changed on release notes and download script.

• release file added:

  • pbta-fusion-putative-oncogenic.tsv
  • pbta-snv-consensus-20191125.zip
  • pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
  • pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
  • pbta-snv-consensus-mutation.maf.tsv.gz
  • pbta-snv-consensus-mutation-tmb.tsv

• release file removed:

  • pbta-gene-expression-rsem-fpkm-collapsed_table.polya.rds
  • pbta-gene-expression-rsem-fpkm-collapsed_table.stranded.rds
  • pbta-snv-consensus_11122019.zip

[jaclyn-taroni]

@yuankunzhu it looks like this includes a zip file of the consensus information:

pbta-snv-consensus-20191125.zip: OK
Archive:  data/pbta-snv-consensus-20191125.zip
   creating: data/snv-consensus-20191125/
  inflating: data/snv-consensus-20191125/consensus_mutation_tmb.tsv  
  inflating: data/snv-consensus-20191125/README.md  
  inflating: data/snv-consensus-20191125/consensus_mutation.maf.tsv 

Can we rename these files and include them in the top directory alongside the other files per this comment #287 (comment)? Copying the relevant part below for your reference:

Regarding the new consensus mutation files, I think since we will probably put the pbta-fusion-putative-oncogenic.tsv directly in the release folder, we should make some changes to how the consensus mutation files are distributed.

The file structure of snv-consensus-20191125.zip is as follows:

 .
├── README.md
├── consensus_mutation.maf.tsv
└── consensus_mutation_tmb.tsv

Could we rename the contents to:
consensus_mutation.maf.tsv -> pbta-snv-consensus-mutation.maf.tsv (+ possibly compress this file)
consensus_mutation_tmb.tsv -> pbta-snv-consensus-mutation-tmb.tsv

And then include these in the "top directory" of the release folder?

[yuankunzhu]

sure thing @jaclyn-taroni.
just made the change, please review.

[jaclyn-taroni]

My apologies, my comment about compressing the MAF file was ambiguous. I would expect that file to be gzipped to be consistent with the other files and then for the unzip steps at lines 51-52 to come out of download-data.sh.

[yuankunzhu]

ah no worries. i was thinking about that too.
so just to be clear, we'd like to have pbta-snv-consensus-mutation.maf.tsv.gz up there instead of pbta-snv-consensus-mutation.maf.tsv.zip?

[jaclyn-taroni]

Yes that’s what I was thinking, thanks.

[jaclyn-taroni]

With 112019e I was mostly checking if edits by maintainers was allowed because I would like the folks that generated the consensus mutation files (@cansavvy, @jashapiro) to include documentation in the README as part of this pull request per #287 (comment) and #287 (comment).

[jaclyn-taroni]

I got the 👍 over on #299, so I will merge those changes into this branch.

[jaclyn-taroni]

👍

[jashapiro]

looks good!