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release notes

current release

release-v14-20200203

  • release date: 2020-02-03

  • status: available

  • changes:

    • Update kallisto stranded file to remove index column per #474. Also removed samples from last re-sequencing polyA+stranded batch that were missed with the v13 release:
      • pbta-gene-expression-kallisto.stranded.rds
    • Update matrices of ependymonal tumor and embryonal tumor fusions of interest by biospecimen from analyses/fusion-summary to include all RNA biospecimens in new pbta-histologies.tsv file without fusion calls. Files updated:
      • fusion_summary_embryonal_foi.tsv
      • fusion_summary_ependymoma_foi.tsv
    • Update Strelka2, Mutect2, and Lancet TCGA MAF files per #483 and #512. Files updated:
      • pbta-tcga-snv-mutect2.vep.maf.gz
      • pbta-tcga-snv-strelka2.vep.maf.gz
      • pbta-tcga-snv-lancet.vep.maf.gz
    • Remove cnv_consensus.tsv file per this comment.
    • Update copy number files:
      • Update CNVkit seg file to add missing specimen per #472:
        • pbta-cnv-cnvkit.seg.gz
      • Update GISTIC results for CNVkit to include missing specimen per #491:
        • pbta-cnv-cnvkit-gistic.zip
      • Add consensus SEG file per #441:
        • pbta-cnv-consensus.seg.gz
      • Add GISTIC results for consensus SEG per #453:
        • pbta-cnv-consensus-gistic.zip
    • Update analysis files and names from exon to cds per #440 and this comment:
      • intersect_strelka_mutect_WGS.bed
      • intersect_cds_lancet.bed
      • intersect_cds_lancet_strelka_mutect_WGS.bed
      • pbta-snv-consensus-mutation-tmb-coding.tsv
    • Update pbta-histologies.tsv to add embryonal molecular_subtypes per #251 using results here and high-grade glioma (HGG) molecular_subtypes per #249 and this commit.
      • Additional clinical data updated include:
        • glioma_brain_region (if sample was not previously classified as glioma)
        • Notes (to concatenate old notes for disease_type_new and molecular_subtype changes and current changes based on OpenPBTA subtyping)
        • disease_type_new
          • HGG: created "Diffuse midline glioma" for any subtype containing DMG and rest were "High-grade glioma". (Previously, DMGs were both HGG and DIPG, but following WHO 2016 nomenclature, we stick with DMG instead of DIPG now that we have subtypes).
            • Embryonal: if molecular_subtype contains ETMR, these became Embryonal tumor with multilayer rosettes while the rest became CNS Embryonal Tumor
        • short_histology
          • HGG: all became HGAT
          • Embryonal: if molecular_subtype contains ETMR, these became ETMR while the rest became Embryonal Tumor
        • broad_histology
          • HGG: all became Diffuse astrocytic and oligodendroglial tumor
          • Embryonal: all became Embryonal Tumor

  • folder structure:

data
└── release-v14-20200203
    ├── release-notes.md
    ├── data-files-description.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.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
    ├── WXS.hg38.100bp_padded.bed
    ├── WXS.hg38.lancet.400bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-consensus.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── pbta-cnv-cnvkit-gistic.zip
    ├── pbta-cnv-consensus-gistic.zip
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-fusion-putative-oncogenic.tsv
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    ├── pbta-sv-manta.tsv.gz
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    ├── independent-specimens.wgswxs.primary.tsv
    ├── pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
    ├── pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    ├── pbta-gene-expression-rsem-tpm.polya.rds
    ├── pbta-gene-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-expression-rsem-tpm.polya.rds
    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-consensus-mutation.maf.tsv.gz
    ├── pbta-snv-consensus-mutation-tmb-all.tsv
    ├── pbta-snv-consensus-mutation-tmb-coding.tsv
    ├── pbta-fusion-recurrently-fused-genes-byhistology.tsv
    ├── pbta-fusion-recurrently-fused-genes-bysample.tsv
    ├── pbta-tcga-snv-lancet.vep.maf.gz
    ├── pbta-tcga-snv-strelka2.vep.maf.gz
    ├── pbta-tcga-snv-mutect2.vep.maf.gz
    ├── pbta-tcga-manifest.tsv
    ├── pbta-mend-qc-results.tar.gz
    ├── pbta-mend-qc-manifest.tsv
    ├── pbta-star-log-final.tar.gz
    ├── pbta-star-log-manifest.tsv
    ├── intersect_cds_lancet_strelka_mutect_WGS.bed
    ├── intersect_cds_lancet.bed
    ├── intersect_strelka_mutect_WGS.bed
    ├── fusion_summary_embryonal_foi.tsv
    └── fusion_summary_ependymoma_foi.tsv

archived releases

release-v13-20200116

  • release date: 2020-01-16
  • status: available
  • changes:
    • Remove stranded RNA-Seq for 23 PNOC samples and 21 CBTTC samples previously sequenced using a polyA library prep and simultaneously address issues #369, #370, and #371. Files updated:
      • pbta-fusion-arriba.tsv.gz
      • pbta-fusion-starfusion.tsv.gz
      • pbta-gene-expression-rsem-tpm.stranded.rds
      • pbta-gene-expression-rsem-fpkm.stranded.rds
      • pbta-isoform-expression-rsem-tpm.stranded.rds
      • pbta-isoform-counts-rsem-expected_count.stranded.rds
      • pbta-gene-counts-rsem-expected_count.stranded.rds
      • pbta-gene-expression-kallisto.stranded.rds
      • pbta-fusion-recurrently-fused-genes-byhistology.tsv
      • pbta-fusion-recurrently-fused-genes-bysample.tsv
      • pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
      • pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    • Add matrices of ependymonal tumor and embryonal tumor fusions of interest by biospecimen from analyses/fusion-summary, subsetted for RNA biospecimens in new pbta-histologies.tsv file. Files added:
      • fusion_summary_embryonal_foi.tsv
      • fusion_summary_ependymoma_foi.tsv
    • Add MendQC and STAR output files and associated manifests, per #341. Files added:
      • pbta-mend-qc-results.tar.gz
      • pbta-mend-qc-manifest.tsv
      • pbta-star-log-final.tar.gz
      • pbta-star-log-manifest.tsv
    • Add TCGA MAF and clinical files per #257. Files added:
      • pbta-tcga-snv-lancet.vep.maf.gz
      • pbta-tcga-snv-mutect2.vep.maf.gz
      • pbta-tcga-snv-strelka2.vep.maf.gz
      • pbta-tcga-manifest.tsv
    • Add cnv_consensus.tsv file from #128.
    • Add analysis files from #351
      • intersect_strelka_mutect_WGS.bed
      • intersect_exon_lancet_strelka_mutect_WGS.bed
      • intersect_exon_WXS.bed
    • Add WXS.hg38.lancet.400bp_padded.bed file.
    • Update pbta-histologies.tsv to remove RNA-Seq samples listed above, propagate medulloblastoma molecular_subtypes per #379, harmonize "Diagnosis" to "Initial CNS Tumor", fix PNOC003 seq_center for RNA-Seq samples to "TGEN", harmonize ethnicity to match CBTTC data in KidsFirst:
Old ethnicity New ethnicity
Non-hispanic Not Hispanic or Latino
Unknown Unavailable/Not Reported
Not Reported Unavailable/Not Reported
  • folder structure:
data
└── release-v13-20200116
    ├── release-notes.md
    ├── data-files-description.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.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
    ├── WXS.hg38.100bp_padded.bed
    ├── WXS.hg38.lancet.400bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── pbta-cnv-cnvkit-gistic.zip
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-fusion-putative-oncogenic.tsv
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    ├── pbta-sv-manta.tsv.gz
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    ├── independent-specimens.wgswxs.primary.tsv
    ├── pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
    ├── pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    ├── pbta-gene-expression-rsem-tpm.polya.rds
    ├── pbta-gene-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-expression-rsem-tpm.polya.rds
    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-consensus-mutation.maf.tsv.gz
    ├── pbta-snv-consensus-mutation-tmb-all.tsv
    ├── pbta-snv-consensus-mutation-tmb-coding.tsv
    ├── pbta-fusion-recurrently-fused-genes-byhistology.tsv
    ├── pbta-fusion-recurrently-fused-genes-bysample.tsv
    ├── pbta-tcga-snv-lancet.vep.maf.gz
    ├── pbta-tcga-snv-strelka2.vep.maf.gz
    ├── pbta-tcga-snv-mutect2.vep.maf.gz
    ├── pbta-tcga-manifest.tsv
    ├── pbta-mend-qc-results.tar.gz
    ├── pbta-mend-qc-manifest.tsv
    ├── pbta-star-log-final.tar.gz
    ├── pbta-star-log-manifest.tsv
    ├── cnv_consensus.tsv
    ├── intersect_exon_lancet_strelka_mutect_WGS.bed
    ├── intersect_exon_WXS.bed
    ├── intersect_strelka_mutect_WGS.bed
    ├── fusion_summary_embryonal_foi.tsv
    └── fusion_summary_ependymoma_foi.tsv

release-v12-20191217

  • release date: 2019-12-17
  • status: available
  • changes:
    • Add data-file-descriptions.md with data release to better track file types, origins, and workflows per #334 and #336
    • Add stranded RNA-Seq for 23 PNOC samples and 21 CBTTC samples previously sequenced using a polyA library prep. Files updated:
      • pbta-fusion-arriba.tsv.gz
      • pbta-fusion-starfusion.tsv.gz
      • pbta-gene-expression-rsem-tpm.stranded.rds
      • pbta-gene-expression-rsem-fpkm.stranded.rds
      • pbta-isoform-expression-rsem-tpm.stranded.rds
      • pbta-isoform-counts-rsem-expected_count.stranded.rds
      • pbta-gene-counts-rsem-expected_count.stranded.rds
      • pbta-gene-expression-kallisto.stranded.rds
      • pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    • Add recurrently-fused genes by histology and matrix of recurrently-fused genes by biospecimen from fusion filtering and prioritization analysis
    • Update consensus TMB files and MAF #333
    • Add RNA-Seq collapsed matrices - wrong files (tables of transcripts removed) were included with V10
    • Rename WGS.hg38.mutect2.unpadded.bed to WGS.hg38.mutect2.vardict.unpadded.bed to better reflect usage
    • Update pbta-histologies.tsv to add new RNA-Seq samples listed above, #222 harmonize disease separators, and reran medulloblastoma classifier using V12 RSEM fpkm collapsed files
      • BS_2Z1MKS84, BS_5VQP0E6K re-classified from Group4 to WNT and BS_3BDAG9YN, BS_8T7DZV2F, and BS_JTMXAMB7 re-classified from Group3 to WNT
    • Add CNVkit GISTIC results focal CN analyses, eg: #244 and #8
  • folder structure:
data
└── release-v12-20191217
    ├── CHANGELOG.md
    ├── data-file-descriptions.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.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
    ├── WXS.hg38.100bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-fusion-putative-oncogenic.tsv
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    ├── pbta-sv-manta.tsv.gz
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    ├── independent-specimens.wgswxs.primary.tsv
    ├── pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
    ├── pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    ├── pbta-gene-expression-rsem-tpm.polya.rds
    ├── pbta-gene-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-expression-rsem-tpm.polya.rds
    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
    ├── pbta-snv-consensus-mutation.maf.tsv.gz
    ├── pbta-snv-consensus-mutation-tmb-all.tsv
    ├── pbta-snv-consensus-mutation-tmb-coding.tsv
    ├── pbta-fusion-recurrently-fused-genes-byhistology.tsv
    └── pbta-fusion-recurrently-fused-genes-bysample.tsv

release-v11-20191126

data
└── release-v11-20191126
    ├── CHANGELOG.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.bed
    ├── WGS.hg38.lancet.300bp_padded.bed
    ├── WGS.hg38.lancet.unpadded.bed
    ├── WGS.hg38.mutect2.unpadded.bed
    ├── WGS.hg38.strelka2.unpadded.bed
    ├── WGS.hg38.vardict.100bp_padded.bed
    ├── WXS.hg38.100bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-fusion-putative-oncogenic.tsv
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    ├── pbta-sv-manta.tsv.gz
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    ├── independent-specimens.wgswxs.primary.tsv
    ├── pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
    ├── pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    ├── pbta-gene-expression-rsem-tpm.polya.rds
    ├── pbta-gene-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-expression-rsem-tpm.polya.rds
    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
    ├── pbta-snv-consensus-mutation.maf.tsv.gz
    └── pbta-snv-consensus-mutation-tmb.tsv

release-v10-20191115

data
└── release-v10-20191115
    ├── CHANGELOG.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.bed
    ├── WGS.hg38.lancet.300bp_padded.bed
    ├── WGS.hg38.lancet.unpadded.bed
    ├── WGS.hg38.mutect2.unpadded.bed
    ├── WGS.hg38.strelka2.unpadded.bed
    ├── WGS.hg38.vardict.100bp_padded.bed
    ├── WXS.hg38.100bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    ├── pbta-sv-manta.tsv.gz
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    ├── independent-specimens.wgswxs.primary.tsv
    ├── pbta-gene-expression-rsem-fpkm-collapsed_table.polya.rds
    ├── pbta-gene-expression-rsem-fpkm-collapsed_table.stranded.rds
    ├── pbta-gene-expression-rsem-tpm.polya.rds
    ├── pbta-gene-expression-rsem-tpm.stranded.rds
    ├── pbta-isoform-expression-rsem-tpm.polya.rds
    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
    └── pbta-snv-consensus_11122019.zip

release-v9-20191105

  • release date: 2019-11-05
  • status: available
  • changes:
    • Updated RNA-Seq FPKM merge files
      • added geneIDs that were missed in previous release
  • folder structure:
data
└── release-v9-20191105
    ├── CHANGELOG.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.bed
    ├── WGS.hg38.lancet.300bp_padded.bed
    ├── WGS.hg38.lancet.unpadded.bed
    ├── WGS.hg38.mutect2.unpadded.bed
    ├── WGS.hg38.strelka2.unpadded.bed
    ├── WGS.hg38.vardict.100bp_padded.bed
    ├── WXS.hg38.100bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    ├── pbta-sv-manta.tsv.gz
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    └── independent-specimens.wgswxs.primary.tsv

release-v8-20191104

  • release date: 2019-11-04
  • status: available
  • changes:
    • Updated clinical file
      • fixed error in primary_site: #214
    • Updated ControlFreeC TSV file
      • added tumor_ploidy and updated genotype to segment_genotype: PR comment
    • Updated RNA-Seq FPKM merge files
      • fixed ID merge error: #221
  • folder structure: same to release-v9-20191105

release-v7-20191031

  • release date: 2019-10-31 🎃

  • status: available

  • changes:

    • update molecular_subtype for the clinical file
    • Add ControlFreeC CNV merged TSV file. data format
    • Add ControlFreeC ploidy to clinical file.
    • Add sample lists for analyses requiring unique patient specimens. issues/155
      • independent-specimens.wgs.primary-plus.tsv
      • independent-specimens.wgswxs.primary-plus.tsv
      • independent-specimens.wgs.primary.tsv
      • independent-specimens.wgswxs.primary.tsv

  • folder structure: same to release-v9-20191105

release-v6-20191030

  • release date: 2019-10-30
  • status: available
  • changes:
    • Clinical file updates:
      • Missing aliquot_id and sample_id added
      • Updated broad_composition to cell line for WGS samples denoted as Cell line
      • Removed duplicate BS_4M0ZMCDC with wrong age at diagnosis
      • Add cohort column for CBTTC or PNOC003 samples
      • Tumor specimens missing composition were changed to Solid Tumor
      • Blood specimens missing primary_site were changed to Peripheral Whole Blood
      • Updated age_at_diagnosis to earliest age reported (same age used in OS calculations)
      • Updated OS_days and OS_status based on updated clinical data
      • Added cancer_predispositions information
      • Added seq_center (could not add seq_instrument at this time due to multiple entries for BS_IDs)
      • Harmonized Diagnosis and Initial CNS Tumor for tumor_descriptor field
      • Changed Relapse sample to Progressive (DIPG sample truly progressive, not relapse)
      • Add tumor purity derived from Theta2 (normal_fraction and tumor_fraction)
      • Add glioma_brain_region for low- and high-grade gliomas ​
    • SV:
      • Removed LUMPY data, as additional benchmarking to remove normal SVs needs to be done. We may not include this in a future release. ​
    • SNV:
      • Re-ran BS_7KR13R3P using targeted panel bed files; removed WXS calls from MAFs
      • Added WXS calls to all MAFs
      • Added targeted panel bed and padded bed files ​
    • CNV:
      • Re-ran ControlFreeC and CNVkit with optional BAF inputs; Added Theta2 purity correction to CNVkit
      • Added copy number to CNVkit and removed ControlFreeC seg file
  • folder structure:
data
└── release-v6-20191030
    ├── CHANGELOG.md
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    ├── StrexomeLite_hg38_liftover_100bp_padded.bed
    ├── WGS.hg38.lancet.300bp_padded.bed
    ├── WGS.hg38.lancet.unpadded.bed
    ├── WGS.hg38.mutect2.unpadded.bed
    ├── WGS.hg38.strelka2.unpadded.bed
    ├── WGS.hg38.vardict.100bp_padded.bed
    ├── WXS.hg38.100bp_padded.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-lancet.vep.maf.gz
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-snv-vardict.vep.maf.gz
    └── pbta-sv-manta.tsv.gz

release-v5-20190924

  • release date: 2019-09-24

  • status: available

  • changes:

  • folder structure:

data
└── release-v5-20190924
    ├── CHANGELOG.md
    ├── md5sum.txt
    ├── WGS.hg38.lancet.300bp_padded.bed
    ├── WGS.hg38.lancet.unpadded.bed
    ├── WGS.hg38.mutect2.unpadded.bed
    ├── WGS.hg38.strelka2.unpadded.bed
    ├── WGS.hg38.vardict.100bp_padded.bed
    ├── WXS.hg38.100bp_padded.bed
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.seg.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-histologies.tsv
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-sv-lumpy.tsv.gz
    ├── pbta-sv-manta.tsv.gz
    ├── pbta-gene-expression-kallisto.polya.rds
    ├── pbta-gene-expression-kallisto.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-gene-counts-rsem-expected_count.polya.rds
    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-snv-lancet.vep.maf.gz
    └── pbta-snv-vardict.vep.maf.gz

release-v4-20190909

  • release date: 2019-09-10
  • status: available
  • changes:
    • Clinical V4:
      • De-duplicated BS_6DCSD5Y6 in the clinical file by removing row with wrong age
      • Added units to age_at_diagnosis column (age_at_diagnosis_days)
    • new RSEM file:
      • Remove QC-failed samples from V3 RSEM.
      • Add BS_XM1AHBDJ which should be included, but was missing from the V3 RSEM
    • new LUMPY file:
      • Add data for 628 more subjects which was missing from V3 LUMPY
  • folder structure:
data
└── release-v4-20190909
    ├── CHANGELOG.md
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.seg.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-gene-expression-kallisto.rds
    ├── pbta-gene-expression-rsem.fpkm.rds
    ├── pbta-histologies.tsv
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-sv-lumpy.tsv.gz
    ├── pbta-sv-manta.tsv.gz
    └── README.md

archived release

release-v3-20190829

release-v2-20190809

  • release date: 2019-08-09
  • status: available
  • changes:
    • removed QC failed RNA-seqs
      • alignment rate < 60%, n=
      • wrong strandedness samples, n=
    • removed tumor/normal genotype mis-match samples
    • removed consent failed samples
    • clincial infomation updated
      • added and harmonized sample ID and diagnosis for PNOC003 samples
      • added medullo subtype information
    • CNV
      • added seg files for CNV data
      • added CNVkit results
    • SV
      • added LUMPY results
      • added annotated SV files
  • folder structure:
data
└── release-v2-20190809
    ├── CHANGELOG.md
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-controlfreec.seg.gz
    ├── pbta-fusion-arriba.tsv.gz
    ├── pbta-fusion-starfusion.tsv.gz
    ├── pbta-gene-expression-kallisto.rds
    ├── pbta-gene-expression-rsem.fpkm.rds
    ├── pbta-histologies.tsv
    ├── pbta-snv-mutect2.vep.maf.gz
    ├── pbta-snv-strelka2.vep.maf.gz
    ├── pbta-sv-lumpy.tsv.gz
    ├── pbta-sv-manta.tsv.gz
    └── README.md

release-v1-20190730

  • release date: 2019-07-30
  • status: not-available as it contains consent/qc failed samples
  • changes: initial push
data
└── release-v1-20190730
    ├── arriba.fusions.tsv.gz
    ├── clinical.tsv
    ├── controlfreec.cnv.tsv.gz
    ├── kallisto.abundance.tsv.gz
    ├── kallisto.genes.list
    ├── manta-sv.tsv.gz
    ├── mutect2.maf.gz
    ├── rsem.genes.list
    ├── rsem.genes.tsv.gz
    ├── rsem.isoforms.tsv.gz
    ├── star-fusion.fusions.tsv.gz
    ├── strelka2.maf.gz
    └── tumor-normal-pair.tsv