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release notes

current release

release-v10

  • release date: 2021-10-11

  • status: available

  • overview of changes:

    • This particular releae added 438 tumor/nomral pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical trials.
    • Usable TCGA RNA-Seq data from diseaseXpress with GDC clinical information are added to (n=10414) were added to the release
    • cnv-consensus-gistic.zip from run-gistic module was added to the release
    • ensg-hugo-rmtl-mapping.tsv is replaced with ensg-hugo-pmtl-mapping.tsv after we switch from RMTL v1.0 to PMTL v1.1
    • All additional changes as well as details about the above 3 changes are as followed.

  • Update histologies file:

    • Add 120 samples from PNOC_dataset_2 (40 WXS tumor, 40 WXS normal and 40 RNA-Seq from 40 patients) and additional 24 PNOC_dataset_1 tumor WGS from 18 samples to release
      • Details see ticket 174
      • After tp53-nf1-scores and run-gistic modules were ran with the base histology file, these samples then ran through molecular-subtyping-HGG, molecular-subtyping-pathology and molecular-subtyping-integrate modules to get their subtype (details also captured below)
      • See ticket 210 for details
    • Add 438 tumor/normal pairs of TARGET ALL WXS samples
    • Change "Known" to "Unknown" in the histologies file since it was mis-coded before
    • Fixed TCGA and GMKF/TARGET OS_days in histology file - see ticket 199
      • For TCGA samples, OS_days column is now populated this way: days_to_death column is preferentially used for OS_days; when it is NA, days_to_last_follow_up is used as long as the value is not negative
      • For TARGET samples that are also present in GMKF cohort, OS_days in TARGET cohort are replaced with OS_days in GMKF cohort since GMKF has more up-to-date records
    • Remove TCGA samples in histology file that is not in the expression matrix or does not have clinical information from GDC portal
    • Additional changes to TCGA histology file - RNA-library of poly-A and sample_type of Tumor (a total of 9551 samples) all have NA composition:
      • For these samples, composition is modified to Solid Tissue as long as primary_site is not NA or Bone Marrow
    • Additionally, there are normal samples in TARGET cohort with broad_histology, short_histology, tumor_descriptor and cancer_group that are not NA
      • For those samples, these fields are changed to NA

  • Use PMTL v1.1 instead of RMTL v1.0 for gene annotation - ensg-hugo-pmtl-mapping.tsv will now be the included in the data release and ensg-hugo-rmtl-mapping.tsv will not longer be used. - Details see ticket 206

  • Run molecular subtyping for new PNOC clinical trials samples

    • Use the merged snv-consensus-plus-hotspots.maf.tsv.gz, consensus_wgs_plus_cnvkit_wxs.tsv.gz, gene-expression-rsem-tpm-collapsed.rds and base histology file to re-run TP53-NF1 module
    • Use the new cnv-consensus.seg.gz and run through GISTIC module
    • Run molecular subtyping for new PNOC sample through HGG, pathology and integrate modules

  • Update cnv-cnvkit.seg.gz, cnv-controlfreec.tsv.gz,consensus_wgs_plus_cnvkit_wxs.tsv.gz, snv-consensus-plus-hotspots.maf.tsv.gz and sv-manta.tsv to include 438 tumor/normal pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical samples.

    • Details for merging PNOC clinical samples see ticket 174
    • Details for merging 438 tumor/normal pairs of TARGET ALL WXS samples see ticket 194

  • Update EFO-MONDO mapped file to remove trailing white space that is causing error

    • Details for merging 438 tumor/nomral pairs of TARGET ALL WXS samples see ticket 208

  • Update gene-counts-rsem-expected_count-collapsed.rds, gene-expression-rsem-tpm-collapsed.rds, fusion-arriba.tsv.gz and fusion-starfusion.tsv.gz with 40 RNA-Seq tumor sample from PNOC_dataset_2 results merged

  • Two TCGA gene expression files, tcga-gene-counts-rsem-expected_count-collapsed.rds and tcga-gene-expression-rsem-tpm-collapsed.rds, for all TCGA in diseaseXpress and has GDC clinical information (n=10414) were now include in data release

  • Update consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz, consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz and consensus_wgs_plus_cnvkit_wxs.tsv.gz files with the following changes:

    • When annotating CNV status, for WXS samples, if WGS was performed on the same sample, we use the germline_sex_estimate from the WGS as the germline_sex_estimate for the WXS samples. Details see ticket 177
    • When matching WGS samples were not available, gender is used as `germline_sex_estimate. Details see ticket 177
    • Additionally, focal-cn-file-preparation module was re-run to include 438 tumor/normal pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical samples. Details see ticket 196

  • cnv-consensus-gistic.zip will now be added to data release after 24 WGS PNOC tumor samples were merged and the module re-run

  • Independent sample lists were re-generated with the following changes:

    • In addition to what are currently in data release, we added scripts to preferentially select WXS tumor when available and the following files will now be added to data release for use by snv-frequencies module - Details see ticket 193
      • independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
      • independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
      • independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
      • independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
    • The independent lists are re-generated with 438 tumor/normal pairs of TARGET ALL WXS samples as well as a total of 144 samples (including WGS, WXS, RNA-Seq for both tumor and normal) from PNOC clinical samples added to the histology file

  • Regenerate fusion-putative-oncogenic.tsv to include results from 40 RNA-Seq tumor samples from PNOC clinical trials - Details see ticket 214

v10
├── 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
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── cnv-consensus.seg.gz
├── cnv-consensus-gistic.zip
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-pmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── tcga-gene-counts-rsem-expected_count-collapsed.rds
├── tcga-gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
├── independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── release-notes.md
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── uberon-map-gtex-group.tsv
└── uberon-map-gtex-subgroup.tsv

archived release

release-v9

  • release date: 2021-09-01
  • status: available
  • overview of changes:
    • This particular release is just an update of efo-mondo-map.tsv per discussion in ticket 182.
    • MONDO and EFO codes were manually reviewed and assigned to cancer_group in OpenPedCan.
v9
├── 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
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-rmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── release-notes.md
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── uberon-map-gtex-group.tsv
└── uberon-map-gtex-subgroup.tsv

archived release

release-v8

  • release date: 2021-08-20
  • status: available
  • overview of changes:
    • This particular release is mainly to include 412 tumor/normal pairs of TARGET WXS samples as listed in ticket 111. Detailed changes see below.
  • detailed changes:

    • Histology file updates - the master ticket is d3b center ticket 43:

      • 412 tumor/normal TARGET WXS samples were included in the histologies.tsv file per ticket 111v
      • sample_id and aliquot_id for some TARGET samples were miscoded before. This release fixed the issue per ticket 145
      • sample_id and aliquot_id were updated using the GTEx coding nomenclature GTEX-[donor ID]-[tissue site ID]-SM-[aliquot ID] (https://www.gtexportal.org/home/faq#sampleIdFormat)
      • primary_site for GTEx samples were updated to match gtex_subgroup column, changing Whole Blood to Blood and Brain - Cerebellar Hemisphere to Brain - Cerebellum
      • broad_histology for TARGET samples were updated as following: Acute Lymphoblastic Leukemia and Acute Myeloid Leukemia were merged to Hematologic malignancy; Clear cell sarcoma of the kidney, Rhabdoid tumor, and Wilms tumor were combined as Renal tumor; Osteosarcoma is changed to Mesenchymal non-meningothelial tumor and Neuroblastoma is converted to Embryonal tumor. See ticket 136 and [ticket 176] (d3b-center/ticket-tracker-OPC#176)
      • For gtex_group == "Cells", the composition column is changed from Solid Tissue to Derived Cell Line per discussion in d3b center ticket 43
      • For short_histology, neuroblastoma samples previously annotated as NBL or Embryonal tumor are converted to Neuroblastoma to be consistent with other samples
      • Updated MB subtypes in the histologies file per ticket 148
      • Some GMKF WGS samples does not have germline_sex_estimate as indicated in ticket 168. Added using the file in the discussion of ticket 159
      • Some TARGET WXS samples miss tumor_ploidy that are actually available - and those samples now have updated ploidy using the file in the discussion session of ticket 160

    • Update DNA related files to include TARGET WXS DNA (412 tumor/normal pairs):

    • Update method to call CNV consensus (WGS) as described in ticket 134 and ticket 149. Briefly, CNV called by MantaSV were filtered to contain only filter == "PASS" before going into the consensus calling workflow. In the subsequent step, instead of only retaining CNV calls that have 50% reciprocal overlap between callers (which was too stringent), the criteria is expanded to include small CNV regions that are 90% covered by a larger CNV. The consensus is the overlapping region.

      • cnv_consensus_seg.gz (WGS samples only - in S3 bucket s3://kf-openaccess-us-east-1-prd-pbta/open-targets/v8/ but not in md5sum.txt file)

    • As a result of changing consensus calling criteria and adding new TARGET WXS DNA sample results to cnv-cnvkit.seg.gz and cnv-controlfreec.tsv.gz, the following files were updated:

      • consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz ticket 159 and ticket 160 (only in S3 bucket s3://kf-openaccess-us-east-1-prd-pbta/open-targets/v8/- not included in automatic download)
      • consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz ticket 159 and ticket 160 (only in S3 bucket s3://kf-openaccess-us-east-1-prd-pbta/open-targets/v8/- not included in automatic download)

    • Added consensus_wgs_plus_cnvkit_wxs.tsv.gz which is a merge of consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz and consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz per ticket 161

    • Updated ensg-hugo-rmtl-mapping.tsv file per ticket 146. The previous release of this file does not contain all gene ENSG IDs and symbols that are present in snv-consensus-plus-hotspots.maf.tsv.gz. This update merged GENCODE V28 and V38 to allow inclusion of more gene ENSG IDs and symbols.

    • Futher update ensg-hugo-rmtl-mapping.tsv PR 48 D3b codes to include all gene ENSG ID to symbol mappings in v7 ensg-hugo-rmtl-mapping.tsv.

    • Update independent samples files to include TARGET WXS DNA (412 tumor/normal pairs) - ticket 165. Previously, these files were not added to our releases. Starting this release, we will also add independent sample list to our release as well.

    • Updated independent samples so that the Kids_First_Biospecimen_ID for allcohorts and eachcohort match if possible: ticket 135

    • Updated independent sample module to arrange by Kids_First_Biospecimen_ID before writing out the file: ticket 179

    • For now, we will add files that are used by analyses modules in this file and these are the following:

      • independent-specimens.wgswxspanel.primary.eachcohort.tsv
      • independent-specimens.wgswxspanel.relapse.eachcohort.tsv
      • independent-specimens.rnaseq.primary.eachcohort.tsv
      • independent-specimens.rnaseq.relapse.eachcohort.tsv
      • independent-specimens.wgswxspanel.primary.tsv
      • independent-specimens.wgswxspanel.relapse.tsv
      • independent-specimens.rnaseq.primary.tsv
      • independent-specimens.rnaseq.relapse.tsv

    • Updated fusion-putative-oncogenic.tsv since at the last step of putative oncogenic fusion filtering, we filter out fusions seen in > 4 broad_histology since they are likely artifacts and with the update of broad_histology, the result will be updated ticket 175

      • fusion-putative-oncogenic.tsv
v8
├── 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
├── cnv-cnvkit.seg.gz
├── cnv-controlfreec.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
├── consensus_wgs_plus_cnvkit_wxs.tsv.gz
├── data-files-description.md
├── efo-mondo-map.tsv
├── ensg-hugo-rmtl-mapping.tsv
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── fusion-putative-oncogenic.tsv
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── histologies.tsv
├── independent-specimens.wgswxspanel.primary.eachcohort.tsv
├── independent-specimens.wgswxspanel.relapse.eachcohort.tsv
├── independent-specimens.rnaseq.primary.eachcohort.tsv
├── independent-specimens.rnaseq.relapse.eachcohort.tsv
├── independent-specimens.wgswxspanel.primary.tsv
├── independent-specimens.wgswxspanel.relapse.tsv
├── independent-specimens.rnaseq.primary.tsv
├── independent-specimens.rnaseq.relapse.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── release-notes.md
├── snv-consensus-plus-hotspots.maf.tsv.gz
├── sv-manta.tsv.gz
├── uberon-map-gtex-group.tsv
└── uberon-map-gtex-subgroup.tsv

archived release

release-v7

  • release date: 2021-07-23
  • status: available
  • changes:
    • Updated EFO/MONDO mapping file per ticket 88
    • Added GTEX UBERON mapping files for subgroup and group per ticket 85
      • Collapsed Cerebellum hemisphere and Cerebellum to Cerebellum since GTEX has the same UBERON code listed for both per ticket 106
      • Renamed Whole Blood to Blood per John Maris's suggestion to alphabetize and ticket 106.
        • Note: v8 gtex lists "whole blood" subgroup and "whole blood" group as UBERON_0013756, which is mapped to venous blood and "Whole blood" maps to UBERON_0000178.
        • After inquiry at GTEx, we were told they are equivalent terms as seen in this link
    • Updated ensg-hugo-rmtl-v1-mapping.tsv with minor updates according to ticket 125 and changed filename to ensg-hugo-rmtl-mapping.tsv
    • Histology file updates:
      • Collapsed Cerebellum hemisphere and Cerebellum to Cerebellum since GTEX has the same UBERON code listed for both per ticket 106
      • Renamed Whole Blood to Blood per John Maris's suggestion to alphabetize and ticket 106.
      • Added inferred strandedness to RNA-Seq samples per ticket 104
      • Added broad_tumor_descriptor to designate grouped Diagnosis and Relapse samples used in SNV, CNV, Fusion tables as well as for grouping on pedcbio per ticket 109
      • Added ploidy information for TARGET AML and NBL WXS samples per ticket 121
      • Collapsed TARGET ids containing suffixes to match the BAM file sample IDs from GDC and match the RDS processed files per comment here
    • Added TARGET NBL and AML WXS, PBTA WXS CNV calls to cnv-cnvkit.seg.gz and cnv-controlfreec.tsv.gz per ticket 80
    • Added consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz (removed WGS only file consensus_seg_annotated_cn_autosomes.tsv.gz) and consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz (removed WGS only file consensus_seg_annotated_cn_x_and_y.tsv.gz) containing consensus WGS and CNVkit WXS data per ticket 102
    • Updated RNA-Seq files to include TARGET RNA (N = 1329) samples:
      • fusion-arriba.tsv.gz
      • fusion-starfusion.tsv.gz
      • fusion-putative-oncogenic.tsv
      • gene-counts-rsem-expected_count-collapsed.rds
      • gene-expression-rsem-tpm-collapsed.rds

archived release

release-v6

  • release date: 2021-06-29
  • status: available
  • changes:
    • Within histologies.tsv:
      • Updated cancer_group logic to make updates as per ticket48
      • combine CBTN+PNOC into cohort == PBTA ticket79
      • GMKF tumor ploidy was added ticket46
      • harmonized tumor_descriptor per ticket61
      • updated clinical info for NBL samples which were missing in source files per ticket43
      • updated experimental_strategy for targeted capture samples per ticket62
    • Add cnv files with PBTA+GMKF samples per ticket44:
      • cnv-cnvkit.seg.gz
      • cnv-controlfreec.tsv.gz
      • cnv-consensus.seg.gz
      • consensus_seg_annotated_cn_autosomes.tsv.gz
      • consensus_seg_annotated_cn_autosomes_xy.tsv.gz
    • Add EFO and MONDO cancer mapping file ticket78:
    • Add ENSG to HUGO mapping file with RMTL designation ticket84 and ticket56

archived release

release-v5

  • release date: 2021-06-17
  • status: available
  • changes:
    • Removed
      • gtex_target_tcga-gene-expression-rsem-tpm-collapsed.polya.rds
      • gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds
    • Update RSEM files to include GTEXv8 files
      • gene-expression-rsem-tpm-collapsed.rds
      • gene-counts-rsem-expected_count-collapsed.rds
    • Update manifest to include GTEx manifest are now v8, TCGA manifest are from GDC and TARGET manifest from Diskin Lab and @afarrel
      • histologies.tsv
    • Added snv PBTA+GMKF maf file
      • snv-consensus-plus-hotspots.maf.tsv.gz
    • Released files below
v5
├── 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
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-counts-rsem-expected_count.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── gene-expression-rsem-tpm.rds
├── histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── snv-consensus-plus-hotspots.maf.tsv.gz
└── release-notes.md

archived release

release-v4

  • release date: 2021-06-01
  • status: available
  • changes:
    • Update rnseq file names to be generic (currently includes PBTA and KFNBL)
      • gene-counts-rsem-expected_count*
      • gene-expression-rsem-tpm*
      • fusion*
    • Added mereged gtex_target_tcga expected_count file
      • gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds
    • Combined PBTA, KFNBL, TARGET, TCGA, GTEX histologies into histologies.tsv
    • Released files below
v4
├── 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
├── fusion-arriba.tsv.gz
├── fusion-starfusion.tsv.gz
├── gene-counts-rsem-expected_count-collapsed.rds
├── gene-counts-rsem-expected_count.rds
├── gene-expression-rsem-tpm-collapsed.rds
├── gene-expression-rsem-tpm.rds
├── gtex_target_tcga-gene-counts-rsem-expected_count-collapsed.rds
├── histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── kfnbl-snv-lancet.vep.maf.gz
├── kfnbl-snv-mutect2.vep.maf.gz
├── kfnbl-snv-strelka2.vep.maf.gz
├── kfnbl-snv-vardict.vep.maf.gz
└── release-notes.md

archived release

release-v3

  • release date: 2021-05-21
  • status: available
  • changes:
    • Update files due to addition of SSF column name
      • kfnbl-snv-vardict.vep.maf.gz
    • Added files for downstream analysis output files from collapse-rnaseq
      • kfnbl-gene-counts-rsem-expected_count-collapsed.stranded.rds
    • Released files below:
v3
├── 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
├── gtex-gene-expression-rsem-tpm-collapsed.polya.rds
├── gtex-histologies.tsv
├── intersect_cds_lancet_strelka_mutect_WGS.bed
├── intersect_strelka_mutect_WGS.bed
├── kfnbl-fusion-arriba.tsv.gz
├── kfnbl-fusion-starfusion.tsv.gz
├── kfnbl-gene-counts-rsem-expected_count-collapsed.stranded.rds
├── kfnbl-gene-counts-rsem-expected_count.stranded.rds
├── kfnbl-gene-expression-kallisto.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds
├── kfnbl-gene-expression-rsem-fpkm.stranded.rds
├── kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds
├── kfnbl-gene-expression-rsem-tpm.stranded.rds
├── kfnbl-histologies.tsv
├── kfnbl-isoform-counts-rsem-expected_count.stranded.rds
├── kfnbl-isoform-expression-rsem-tpm.stranded.rds
├── kfnbl-snv-lancet.vep.maf.gz
├── kfnbl-snv-mutect2.vep.maf.gz
├── kfnbl-snv-strelka2.vep.maf.gz
├── kfnbl-snv-vardict.vep.maf.gz
├── release-notes.md
├── target-gene-expression-rsem-tpm-collapsed.rds
├── target-histologies.tsv
├── tcga-gene-expression-rsem-tpm-collapsed.rds
└── tcga-histologies.tsv

archived release

release-v2

  • release date: 2021-05-18
  • status: available
  • changes:
    • Updated rnaseq files with addition of BS_ETC8R0TD
      • kfnbl-fusion-arriba.tsv.gz
      • kfnbl-fusion-starfusion.tsv.gz
      • kfnbl-gene-counts-rsem-expected_count.stranded.rds
      • kfnbl-gene-expression-kallisto.stranded.rds
      • kfnbl-gene-expression-rsem-fpkm.stranded.rds
      • kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds
      • kfnbl-gene-expression-rsem-tpm.stranded.rds
      • kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds
      • kfnbl-isoform-counts-rsem-expected_count.stranded.rds
      • kfnbl-isoform-expression-rsem-tpm.stranded.rds
      • kfnbl-histologies.tsv
    • Released files below:
open-targets
└── v2
    ├── gtex-gene-expression-rsem-tpm-collapsed.polya.rds
    ├── gtex-histologies.tsv
    ├── intersect_cds_lancet_strelka_mutect_WGS.bed
    ├── intersect_strelka_mutect_WGS.bed
    ├── md5sum.txt
    ├── kfnbl-fusion-arriba.tsv.gz
    ├── kfnbl-fusion-starfusion.tsv.gz
    ├── kfnbl-gene-counts-rsem-expected_count.stranded.rds
    ├── kfnbl-gene-expression-kallisto.stranded.rds
    ├── kfnbl-gene-expression-rsem-fpkm.stranded.rds
    ├── kfnbl-gene-expression-rsem-fpkm-collapsed.stranded.rds
    ├── kfnbl-gene-expression-rsem-tpm.stranded.rds
    ├── kfnbl-gene-expression-rsem-tpm-collapsed.stranded.rds
    ├── kfnbl-isoform-counts-rsem-expected_count.stranded.rds
    ├── kfnbl-isoform-expression-rsem-tpm.stranded.rds
    ├── kfnbl-histologies.tsv    
    ├── kfnbl-snv-lancet.vep.maf.gz
    ├── kfnbl-snv-mutect2.vep.maf.gz
    ├── kfnbl-snv-strelka2.vep.maf.gz
    ├── kfnbl-snv-vardict.vep.maf.gz
    ├── release-notes.md 
    ├── target-gene-expression-rsem-tpm-collapsed.rds
    ├── target-histologies.tsv
    ├── tcga-gene-expression-rsem-tpm-collapsed.rds
    ├── tcga-histologies.tsv
    ├── 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

archived release

release-v1

  • release date: 2021-04-21
  • status: available
  • changes:
    • Added files below:
open-targets
└── v1
    ├── intersect_cds_lancet_strelka_mutect_WGS.bed
    ├── intersect_strelka_mutect_WGS.bed
    ├── md5sum.txt
    ├── kfnbl-gene-counts-rsem-expected_count.stranded.rds
    ├── kfnbl-gene-expression-rsem-fpkm.stranded.rds
    ├── kfnbl-gene-expression-rsem-tpm.stranded.rds
    ├── kfnbl-histologies.tsv    
    ├── kfnbl-snv-lancet.vep.maf.gz
    ├── kfnbl-snv-mutect2.vep.maf.gz
    ├── kfnbl-snv-strelka2.vep.maf.gz
    ├── kfnbl-snv-vardict.vep.maf.gz
    ├── release-notes.md
    ├── 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