Planned release: v15

[kgaonkar6]

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

Updated fusion files, TCGA MAFs, clinical file

What release are you using?

v14

Put your question or report your issue here.

Fusion files need to be updated because of updated kinase reference list and old v13 recurrently-fused-genes files in v14

• pbta-fusion-recurrently-fused-genes-byhistology.tsv per comment and Fusion Filtering ("other" reading frame ) edits  #553
• pbta-fusion-putative-oncogenic.tsv per Updated analysis: Update kinase reference gene list for fusion filtering  #530 , Fusion Filtering ("other" reading frame ) edits  #553 and comment
• pbta-fusion-recurrently-fused-genes-bysample.tsv per [comment] (edit to reference gene list #539 (comment)) and Fusion Filtering ("other" reading frame ) edits  #553
• TCGA MAFs per Proposed Analysis: Run brain TCGA SNV data through PBTA SNV caller pipeline #257 using BED file from WXS kit
• pbta-histologies.tsv per v14 PBTA Histologies #541 and possibly add EPN subtypes from Ependymoma subtyping #490

[jharenza]

@jaclyn-taroni should there be any updates to GISTIC/CN files in V15? We are probably looking at another week or so until we can do a release.

[cansavvy]

@kgaonkar6, when you say BED file from WXS kit does that mean using the WXS file: WXS.hg38.100bp_padded.bed from the data release?

[jaclyn-taroni]

@jharenza re: GISTIC/CN files - I would recommend that we use the consensus GISTIC file in master for consistency's sake: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/46cf6ccb119312ccae6122ac94c51710df01f6da/analyses/run-gistic/results/pbta-cnv-consensus-gistic.zip

We can also think about distributing the consensus files here: https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/46cf6ccb119312ccae6122ac94c51710df01f6da/analyses/focal-cn-file-preparation/results

[jharenza]

@cansavvy no, the BED file from your comment here: #521 (comment)

(sorry, I updated the comment from @kgaonkar6 to be inclusive for v15)

[jharenza]

@adamcresnick suggests we change disease_type_old and disease_type_new to not sound so much like right/wrong/QC, but to reflect all information: pathology_diagnosis and integrated_diagnosis, so will update with v15

[jharenza]

@yuankunzhu fyi for next release

[jharenza]

@jaclyn-taroni - For:

We can also think about distributing the consensus files here: https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/46cf6ccb119312ccae6122ac94c51710df01f6da/analyses/focal-cn-file-preparation/results

You are talking about these two files, correct?

consensus_seg_annotated_cn_autosomes.tsv.gz
consensus_seg_annotated_cn_x_and_y.tsv.gz

[jaclyn-taroni]

Yes @jharenza, that's correct.

[jharenza]

Looping in @yuankunzhu and @tkoganti to this thread.

[jharenza]

@jashapiro @jaclyn-taroni do we still want pbta-cnv-cnvkit-gistic.zip in the data release since we have consensus? right now, that one was processed on d3b's end, so it points to the bash code in our repo, but since we are replacing pbta-cnv-consensus-gistic.zip with the GISTIC in docker here, would you also want to update the cnvkit gistic results if we keep them?

[jharenza]

closed via #569