release notes

current release

release-v16-20200320

release date: 2020-03-27
status: available
changes:
- Updated TCGA MAFs per #568
- Update TCGA manifest file to include BED file used per sample
- Add new TCGA BED files, padded and unpadded
- Remove old TCGA BED file gencode.v19.basic.exome.hg38liftover.100bp_padded.bed
- new fusions files from #621:
  - pbta-fusion-putative-oncogenic.tsv
  - pbta-fusion-recurrently-fused-genes-byhistology.tsv
  - pbta-fusion-recurrently-fused-genes-bysample.tsv
- new fusion summarys from analyses/fusion-summary
  - fusion_summary_ewings_foi.tsv
folder structure:

data
└── release-v16-20200320
    ├── consensus_seg_annotated_cn_autosomes.tsv.gz
    ├── consensus_seg_annotated_cn_x_and_y.tsv.gz
    ├── data-files-description.md
    ├── fusion_summary_embryonal_foi.tsv
    ├── fusion_summary_ependymoma_foi.tsv
    ├── fusion_summary_ewings_foi.tsv
    ├── independent-specimens.wgs.primary-plus.tsv
    ├── independent-specimens.wgs.primary.tsv
    ├── independent-specimens.wgswxs.primary-plus.tsv
    ├── independent-specimens.wgswxs.primary.tsv
    ├── intersect_cds_lancet_strelka_mutect_WGS.bed
    ├── intersect_cds_lancet_WXS.bed
    ├── intersect_strelka_mutect_WGS.bed
    ├── md5sum.txt
    ├── pbta-cnv-cnvkit-gistic.zip
    ├── pbta-cnv-cnvkit.seg.gz
    ├── pbta-cnv-consensus-gistic.zip
    ├── pbta-cnv-consensus.seg.gz
    ├── pbta-cnv-controlfreec.tsv.gz
    ├── 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.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-collapsed.polya.rds
    ├── pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
    ├── pbta-gene-expression-rsem-fpkm.polya.rds
    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
    ├── pbta-gene-expression-rsem-tpm.polya.rds
    ├── pbta-gene-expression-rsem-tpm.stranded.rds
    ├── pbta-histologies.tsv
    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
    ├── pbta-isoform-expression-rsem-tpm.polya.rds
    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
    ├── pbta-mend-qc-manifest.tsv
    ├── pbta-mend-qc-results.tar.gz
    ├── pbta-snv-consensus-mutation.maf.tsv.gz
    ├── pbta-snv-consensus-mutation-tmb-all.tsv
    ├── pbta-snv-consensus-mutation-tmb-coding.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-star-log-final.tar.gz
    ├── pbta-star-log-manifest.tsv
    ├── pbta-sv-manta.tsv.gz
    ├── pbta-tcga-manifest.tsv
    ├── pbta-tcga-snv-lancet.vep.maf.gz
    ├── pbta-tcga-snv-mutect2.vep.maf.gz
    ├── pbta-tcga-snv-strelka2.vep.maf.gz
    ├── release-notes.md
    ├── StrexomeLite_hg38_liftover_100bp_padded.bed
    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.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
    ├── intersected_whole_exome_agilent_designed_120_AND_tcga_6k_genes.Gh38.bed
    ├── intersected_whole_exome_agilent_plus_tcga_6k_AND_tcga_6k_genes.Gh38.bed
    ├── tcga_6k_genes.targetIntervals.Gh38.bed
    ├── tcga_6k_genes.targetIntervals.bed
    ├── whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.Gh38.bed
    ├── whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.bed
    ├── whole_exome_agilent_designed_120.targetIntervals.Gh38.bed
    ├── whole_exome_agilent_designed_120.targetIntervals.bed
    ├── whole_exome_agilent_plus_tcga_6k.targetIntervals.Gh38.bed
    └── whole_exome_agilent_plus_tcga_6k.targetIntervals.bed

archived release

release-v15-20200228

release date: 2020-02-28
status: available
changes:
- Update Strelka2, Mutect2, and Lancet TCGA MAF files per #257; files updated:
  - pbta-tcga-snv-mutect2.vep.maf.gz
  - pbta-tcga-snv-strelka2.vep.maf.gz
  - pbta-tcga-snv-lancet.vep.maf.gz
- Add TCGA WXS BED regions file lifted from hg19 to hg38 and padded by 100bp, which was used for variant calling:
  - gencode.v19.basic.exome.hg38liftover.100bp_padded.bed, obtained from the GDC website; NOTE: this BED file is almost certainly wrong per #568.
- Replace pbta-cnv-consensus-gistic.zip with the file from the OpenPBTA analysis master repository now that GISTIC has been installed comment.
- Updated pbta-histologies.tsv to:
  - Harmonize Embryonal Tumor and Embryonal tumor #541
  - Change disease_type_old to pathology_diagnosis and disease_type_new to integrated_diagnosis per request in comment.
- Add consensus focal CN files from analysis:
  - consensus_seg_annotated_cn_autosomes.tsv.gz
  - consensus_seg_annotated_cn_x_and_y.tsv.gz
- Updated fusion files to add additional kinase genes, remove residual polyA stranded samples, andfix order of filtering operations per comment, comment, #530, and #553, and PR #567:
  - pbta-fusion-recurrently-fused-genes-byhistology.tsv
  - pbta-fusion-putative-oncogenic.tsv
  - pbta-fusion-recurrently-fused-genes-bysample.tsv
folder structure:

data
└── release-v15-20200228
    ├── 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
    ├── gencode.v19.basic.exome.hg38liftover.100bp_padded.bed
    ├── consensus_seg_annotated_cn_autosomes.tsv.gz
    └── consensus_seg_annotated_cn_x_and_y.tsv.gz

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

release date: 2019-11-26
status: available
changes:
- Add putative oncogenic fusions from fusion filtering and prioritization analysis
- Update consensus SNV/indels to contain consensus MNVs
- Add RNA-Seq collapsed matrices - wrong files (tables of transcripts removed) were included with V10
folder structure:

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

release date: 2019-11-15
status: available
changes:
- Add RNA-Seq GTF and fasta files per ticket here
- Add RSEM gene TPM and isoform matrices
- Add SNV consensus files
- Add new MAFs for lancet, vardict, mutect2 -reran VCF2MAF to harmonize columns
- Add Collapsed RNA matrices
folder structure:

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:
- Separated RNA-Seq files:
  - Created separate RDS files for stranded and polyA RNA-Seq samples
- new RNA-Seq counts files:
  - Added RSEM count matrices for genes and transcripts
- new ARRIBA file:
  - Add annots column header which was removed during FusionAnnotator run
- new SNV files:
  - Add Lancet VEP-annotated MAF
  - Add VarDict VEP-annotated MAF
- new BED interval files:
  - Add WXS BED (same file used for each variant caller)
  - Add WGS BED files for each variant caller
  - Methods described here.
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 date: 2019-08-29
status: available
changes:
- Arriba fusions run with https://github.com/FusionAnnotator/CTAT_HumanFusionLib/wiki#red-herrings-fusion-pairs-that-may-not-be-relevant-to-cancer-and-potential-false-positives to match STAR-fusion results
- Clinical data sheet, added information for:
  - germline_sex_estimate
  - overall survival (days)
  - overall survival status (living/deceased)
  - RNA_library type
  - edited previous sex variable to be reported_gender
folder structure: same to release-v4-20190909

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

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release-notes.md

release-notes.md

release notes

current release

release-v16-20200320

archived release

release-v15-20200228

release-v14-20200203

archived releases

release-v13-20200116

release-v12-20191217

release-v11-20191126

release-v10-20191115

release-v9-20191105

release-v8-20191104

release-v7-20191031

release-v6-20191030

release-v5-20190924

release-v4-20190909

archived release

release-v3-20190829

release-v2-20190809

release-v1-20190730

Files

release-notes.md

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release-notes.md

File metadata and controls

release notes

current release

release-v16-20200320

archived release

release-v15-20200228

release-v14-20200203

archived releases

release-v13-20200116

release-v12-20191217

release-v11-20191126

release-v10-20191115

release-v9-20191105

release-v8-20191104

release-v7-20191031

release-v6-20191030

release-v5-20190924

release-v4-20190909

archived release

release-v3-20190829

release-v2-20190809

release-v1-20190730