v13 release - Githubissues

Which new datasets are being added with this release?

CPTAC and HOPE AYA proteomics CMI (Count Me In) RNA-Seq Remaining X01 samples HOPE AYA tumor only DNA

What is the sample breakdown (number of WGS, WXS, RNA-Seq, Panel, Methylation, other)?

> as.data.frame(table(v13_base$experimental_strategy))
                   Var1  Freq
1           Methylation  2656
2    Phospho-Proteomics   308
3               RNA-Seq 31908
4             snRNA-Seq     2
5   Targeted Sequencing  2526
6                   WGS  5376
7 Whole Cell Proteomics   308
8                   WXS  2615

by cohort:

> table(v13_base$sub_cohort, v13_base$experimental_strategy)               
                Methylation Phospho-Proteomics RNA-Seq snRNA-Seq Targeted Sequencing   WGS Whole Cell Proteomics   WXS
  CBTN                 1799                  0    1034         2                   0  1650                     0     0
  Chordoma                0                  0     128         0                   0     2                     0     7
  CPTAC                   0                218       0         0                   0     0                   218     0
  DGD                     0                  0       0         0                1526     0                     0     0
  HOPE                   78                 90      85         0                   0   153                    90     0
  Kentucky                0                  0       0         0                   0     3                     0     0
  Maris                   0                  0      40         0                   0     0                     0     0
  Mioncoseq               0                  0     133         0                   0     0                     0   277
  NBL-X01-FY16            0                  0     196         0                   0   671                     0     0
  Oligo                   0                  0      60         0                   0   119                     0     0
  PBTA-X01-FY22           0                  0     796         0                   0  2651                     0     0
  PNOC                    0                  0      91         0                   2   127                     0   177
  PPTC                    0                  0     243         0                   0     0                     0     0
  TARGET                779                  0    1309         0                 998     0                     0  2154
  TCGA                    0                  0   10411         0                   0     0                     0     0

What module(s) generated any new files to include in the release? Has that module been added to the analysis/README.md, and to CI?

No new modules, but there will be a new QC metrics file contained in the release:

rna-dna-qc-stats-full.tsv

Are you aware of any modules impacted by the file(s) change(s)? Describe if the file name is changed.

HGG subtyping was modified since last release, create subset files will be updated

What data file(s) are added/updated/removed in this release?

[Pre-release files]

[ ] histologies-base.tsv
[ ] cnv-cnvkit.seg.gz
[ ] cnvkit_with_status.tsv
[ ] cnv-controlfreec.tsv.gz
[ ] cnv-consensus-gistic.zip
[ ] cnv-consensus.seg.gz
[ ] consensus_seg_with_status.tsv
[ ] consensus_wgs_plus_cnvkit_wxs.tsv.gz
[ ] consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
[ ] consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
[ ] fusion-arriba.tsv.gz
[ ] fusion-dgd.tsv.gz
[ ] fusion-putative-oncogenic.tsv
[ ] fusion-starfusion.tsv.gz
[ ] fusion_summary_embryonal_foi.tsv
[ ] fusion_summary_ependymoma_foi.tsv
[ ] fusion_summary_ewings_foi.tsv
[ ] fusion_summary_lgat_foi.tsv
[ ] rna-dna-qc-stats-full.tsv
[ ] snv-consensus-plus-hotspots.maf.tsv.gz
[ ] snv-dgd.maf.tsv.gz
[ ] sv-manta.tsv.gz
[ ] snv-mutation-tmb-all.tsv
[ ] snv-mutation-tmb-coding.tsv
[ ] gene-expression-rsem-tpm-collapsed.rds
[ ] gene-counts-rsem-expected_count-collapsed.rds
[ ] tcga-gene-expression-rsem-tpm-collapsed.rds
[ ] tcga-gene-counts-rsem-expected_count-collapsed.rds
[ ] rna-isoform-expression-rsem-tpm.rds
[ ] methyl-m-values.rds
[ ] methyl-cn-values.rds
[ ] methyl-beta-values.rds
[ ] independent-specimens.rnaseq.primary-plus.pre-release.tsv
[ ] independent-specimens.rnaseq.primary.pre-release.tsv
[ ] independent-specimens.rnaseq.relapse.pre-release.tsv

[Commit files]

[ ] histologies.tsv
[ ] efo-mondo-map.tsv
[ ] ensg-hugo-pmtl-mapping.tsv
[ ] uberon-map-gtex-group.tsv
[ ] uberon-map-gtex-subgroup.tsv
[ ] independent-specimens.methyl.primary-plus.eachcohort.tsv
[ ] independent-specimens.methyl.primary-plus.tsv
[ ] independent-specimens.methyl.primary.eachcohort.tsv
[ ] independent-specimens.methyl.primary.tsv
[ ] independent-specimens.methyl.relapse.eachcohort.tsv
[ ] independent-specimens.methyl.relapse.tsv
[ ] independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
[ ] independent-specimens.rnaseqpanel.primary-plus.tsv
[ ] independent-specimens.rnaseqpanel.primary.eachcohort.tsv
[ ] independent-specimens.rnaseqpanel.primary.tsv
[ ] independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
[ ] independent-specimens.rnaseqpanel.relapse.tsv
[ ] independent-specimens.wgs.primary-plus.eachcohort.tsv
[ ] independent-specimens.wgs.primary-plus.tsv
[ ] independent-specimens.wgs.primary.eachcohort.tsv
[ ] independent-specimens.wgs.primary.tsv
[ ] independent-specimens.wgs.relapse.eachcohort.tsv
[ ] independent-specimens.wgs.relapse.tsv
[ ] independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
[ ] independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
[ ] independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
[ ] independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
[ ] independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
[ ] independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
[ ] independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
[ ] independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
[ ] independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
[ ] independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
[ ] independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
[ ] independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv

[Bed files and sample mapping]

[ ] biospecimen_id_to_bed_map.txt
[ ] ashion_exome_v2_targets_hg38_padded100.bed
[ ] hg38_strelka.bed
[ ] intersect_cds_lancet_strelka_mutect_WGS.bed
[ ] intersect_strelka_mutect_WGS.bed
[ ] nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
[ ] S0274956_Padded_HG38.merged.bed
[ ] S02972011_Covered_hg38_100.bed
[ ] S04380110_Regions_hg38_100.bed
[ ] S07604715_100bp_Padded.bed
[ ] SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
[ ] StrexomeLite_hg38_liftover_100bp_padded.bed
[ ] Strexome_targets_intersect_sorted_padded100.GRCh38.bed
[ ] TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
[ ] truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
[ ] wgs_canonical_calling_regions.hg38.bed
[ ] WGS.hg38.lancet.300bp_padded.bed
[ ] WGS.hg38.lancet.unpadded.bed
[ ] WGS.hg38.mutect2.vardict.unpadded.bed
[ ] WGS.hg38.strelka2.unpadded.bed
[ ] WGS.hg38.vardict.100bp_padded.bed
[ ] xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

[File descriptions and notes]

[ ] data-files-description.md
[ ] release-notes.md

d3b-center / OpenPedCan-analysis

v13 release #469

Which new datasets are being added with this release?

What is the sample breakdown (number of WGS, WXS, RNA-Seq, Panel, Methylation, other)?

What module(s) generated any new files to include in the release? Has that module been added to the analysis/README.md, and to CI?

Are you aware of any modules impacted by the file(s) change(s)? Describe if the file name is changed.

What data file(s) are added/updated/removed in this release?

Any additional notes to add for discussion?