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v12 release #431

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ewafula opened this issue Oct 12, 2022 · 1 comment
Closed

v12 release #431

ewafula opened this issue Oct 12, 2022 · 1 comment
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ticket in progress v12

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@ewafula
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ewafula commented Oct 12, 2022 •
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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?

[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-annoFuse.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_lgg_hgg_foi.tsv
  • snv-consensus-plus-hotspots.maf.tsv.gz
  • snv-dgd.maf.tsv.gz
  • splice-events-rmats.tsv.gz Create merged rMATs matrix for v13 release #480
  • 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
  • methyl-md5sum.txt
  • 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-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
  • 20038D-17Q6-01.regions.bed
  • agilent-v4-targets-ucsc.bed
  • onco1500-v2-targets-ucsc.bed
  • onco1500-v4-targets-ucsc.bed
  • onco1500-v6-targets-ucsc.bed
  • onco1500-v6a-targets-ucsc.bed

[Methylation arrays metadata]

  • infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip
  • infinium.gencode.v39.probe.annotations.tsv.gz

[File descriptions and notes]

  • data-files-description.md
  • release-notes.md

Any additional notes to add for discussion?
@ewafula ewafula added the v12 label Oct 12, 2022
This was referenced Apr 13, 2023
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@jharenza
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jharenza commented May 1, 2023

Closed with d3b-center/OpenPedCan-analysis#321

@jharenza jharenza closed this as completed May 1, 2023
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