v15 data release - update TCGA and GTEX count and TPM matrices

Which new datasets are being added with this release?

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

Same as v14

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?

GTEX and TCGA counts and TPM matrices will be updated

[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
[ ] 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

Any additional notes to add for discussion?

After discussions between @komalsrathi , Diskin Lab, @migbro, and @zhangb1 , we found that the collapse-rnaseq post GTEX and TCGA liftover has a bug in that there are genes missing from the collapsed count and tpm matrices. For example, "CD99" in the below pre-collapse counts file for TCGA:

> tcga_counts_not_collapsed %>%
+   filter(grepl("CD99", gene_name)) %>%
+   select(gene_name, `TCGA-02-0047-01A-01R-1849-01`, `TCGA-02-0055-01A-01R-1849-01`)
# A tibble: 5 × 3
  gene_name `TCGA-02-0047-01A-01R-1849-01` `TCGA-02-0055-01A-01R-1849-01`
  <chr>                              <dbl>                          <dbl>
1 CD99L2                              6159                           5116
2 CD99P1                                 0                              0
3 CD99                                   0                              0
4 CD99P1                                96                            317
5 CD99                               23661                          36155

But after collapse, only CD99L2 exists.

We would like to update these 4 files to contain all genes which are non-0.

d3b-center / OpenPedCan-analysis