data release v7

[jharenza]

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

List of updates for v7

What release are you using?

v6

Put your question or report your issue here.

Update data files

• merge v7 consensus SNV and CNV files #100
• Merge Consensus annotated CNV + CNVKit annotated WXS only samples as a new data file
• Merge seg files cnv-consensus.seg.gz + cnv-cnvkit.seg.gz as new data file
• Proposed Analysis: WXS cnv annotated seg file generation #102
• Create merge RNA-Seq files for v7 (v6 + new TARGET RNA) #101
• Proposed Analysis: fusion_filtering rerun for v7 #126
• Merge GTEx TPM and expected_count to PBTA+GMKF+TARGET merged files
• Update EFO MONDO file #88
• Update data-files-description.md for v7 #117
• Updated analysis: mb subtyping to use medullo-classifier results #116 save for v8
• Update ensg-hugo-rmtl-mapping.tsv in v7 #125

Update histologies.tsv add PR with updates in https://github.com/d3b-center/D3b-codes

• Create Table with Uberon codes for GTEx Subgroups #85
• v6 histologies.tsv has missing RNA_library values for some RNA-Seq samples #104
• Collapse two cerebellum subgroups to one for GTEX, update blood #106
• v6 histologies.tsv add broad_tumor_descriptor #109
• Histology file miss tumor_ploidy information #121
• We should remove all TARGET RNA samples not included within the GDC overlap per [this ticket]
  (Proposed Analysis: Run KF Pipelines on TARGET RNA #9 (comment)) so that we aren't inadvertently choosing independent samples which are not in our sequencing files.
• Generate md5sum

[kgaonkar6]

For transcriptomic-dimension-reduction we will need the following files should we add this to v7? Or should we just do tpm only?

gene-expression-rsem-fpkm.rds
gene-expression-kallisto.rds

[jharenza]

For transcriptomic-dimension-reduction we will need the following files should we add this to v7? Or should we just do tpm only?

gene-expression-rsem-fpkm.rds
gene-expression-kallisto.rds

is this only for the BRAF mutant clustering of HGGs to determine LGG status? If so, I think we can maybe omit that code for the subtyping?

[kgaonkar6]

It's only for the BRAF mutant clustering, I'm ok to remove it from subtyping 👍

[jharenza]

I updated the release notes for the EFO/MONDO and uberon files, so you can update based on what is uploaded now to s3.

[jharenza]

closing with PR 61