Planned release: V19

[jharenza]

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

pbta-histologies.tsv
all RNA-Seq files

What release are you using?

V18

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

NA

Remove BS_JXF8A2A6 from dataset per #862

• pbta-star-log-final.tar.gz
• pbta-star-log-manifest.tsv
• pbta-mend-qc-manifest.tsv
• pbta-mend-qc-results.tar.gz
• pbta-isoform-counts-rsem-expected_count.stranded.rds
• pbta-isoform-expression-rsem-tpm.stranded.rds
• pbta-fusion-arriba.tsv.gz
• pbta-fusion-putative-oncogenic.tsv
• pbta-fusion-recurrently-fused-genes-byhistology.tsv
• pbta-fusion-recurrently-fused-genes-bysample.tsv
• pbta-fusion-starfusion.tsv.gz
• pbta-gene-counts-rsem-expected_count.stranded.rds
• pbta-gene-expression-kallisto.stranded.rds
• pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
• pbta-gene-expression-rsem-fpkm.stranded.rds
• pbta-gene-expression-rsem-tpm.stranded.rds
• independent-specimens.rnaseq.primary-plus-stranded.tsv
• fusion_summary_lgat_foi.tsv
• pbta-histologies-base.tsv
• pbta-histologies.tsv
• md5sum.txt

Add new medulloblastoma subtype pathology results file #746

Update all molecular subtypes, broad_histologies, short_histologies, and integrated_diagnoses.

[jaclyn-taroni]

I am not sure that this issue is totally up to date, but I did want to make note of something that will need to be included in the v19 release.

We anticipate that there will be new LGAT subtyping information that can be included in v19. One of the multiple LGAT subtyping pull requests (#842) was merged before v18 went out, but we did not want to hold up v18 for all of the LGAT pull request (see: #847 (comment)). The results files going in as part of #896 will not include new LGAT subtyping information, but the code base will reflect that #842 went in.

[jharenza]

• Add PFS_days to histologies file per Time to progression in addition to time to death?  #963
• Add scavenged hotspot + consensus maf per Proposed Analysis: add scavenging of cancer hotspots to consensus SNV calls #819
• possibly update CNV files per add fpkm matrix; add note about ControlFreeC CN #43 (TBD) - will now be in V20
• Rerun all subtyping
• Add MB file needed for Updated analysis: medulloblastoma consensus subtypes #747

[kgaonkar6]

Just documenting some file updates for the v19 release:

@migbro added updated maf files for pbta and tcga

• pbta-tcga-snv-mutect2.vep.maf.gz
• pbta-tcga-snv-lancet.vep.maf.gz
• pbta-tcga-snv-strelka2.vep.maf.gz
• pbta-snv-lancet.vep.maf.gz
• pbta-snv-strelka2.vep.maf.gz
• pbta-snv-mutect2.vep.maf.gz
• pbta-snv-vardict.vep.maf.gz

@jashapiro added the consensus files based on the updated MAFs to https://open-pbta.s3.us-east-1.amazonaws.com/data/snv-consensus/snv-consensus-20210427.zip. The files being updated are:

• pbta-snv-consensus-mutation.maf.tsv.gz
• pbta-snv-consensus-mutation-tmb-all.tsv
• pbta-snv-consensus-mutation-tmb-coding.tsv
• tcga-snv-consensus-snv.maf.tsv.gz
• tcga-snv-mutation-tmb-all.tsv
• tcga-snv-mutation-tmb-coding.tsv

[jharenza]

closed with #1026