Planned data release: V12

[jharenza]

What data file(s) does this issue pertain to?

data release v12

What release are you using?

NA

Put a link to the relevant section of the OpenPBTA-manuscript here.

NA

Put your question or report your issue here.

Will add:

• newly sequenced and processed stranded RNA-Seq for 23 PNOC samples and 21 CBTTC samples - will update expression files, fusion files
• updated clinical file to capture BS_IDs from above samples
• GISTIC results for CNVkit (Proposed Analysis: Molecularly subtype ATRT tumors #244) - comment here
• recurrently-fused genes list by patient and histology Planned Analysis: Analysis of recurrent fusions #10
• updated TMB files PR 2 of 3 TMB calculation revamp #311 PR 1 of 3 TMB revamp: Separate TMB calculations as "coding only" and "all" #307

@jaclyn-taroni - we will have to re-release consensus rna-seq files and fusion files in a subsequent release. should we do this immediately after v12 or do a "silent" v12 in which we run these analyses, then a public v13 to capture all of the changes?

[jaclyn-taroni]

Summarizing a conversation from Slack: The consensus fusion and collapsed RNA-seq files will be included in the v12 release as someone will run the collapse-rnaseq module (instructions here) and fusion_filtering module upstream of the release.

[cansavvy]

A zip file with the updated TMB and consensus files are added to S3 in openpbta/snv-consensus. (date: 2019-12-12)

Changes:

• SNV consensus analysis is re-ran with v11 data.
• TMB is separated into coding only and all mutations TMB files using the new consensus TSV.

[jharenza]

openpbta/snv-consensus

@cansavvy can you send me the direct S3 link? I know it was in an old PR but can't readily find it.

[cansavvy]

openpbta/snv-consensus

@cansavvy can you send me the direct S3 link? I know it was in an old PR but can't readily find it.

https://open-pbta.s3.amazonaws.com/data/snv-consensus/snv-consensus-20191212.zip

[cansavvy]

I see a bit of conversation occurred about the snv consensus file names while I was gone: #293 Would you like me to change the file names on S3 to fit the new convention?

[jharenza]

@cansavvy, nah, we can rename since that file is also being hosted on the same bucket as the other v12 data

[jaclyn-taroni]

Closed via #347