This document contains information about all data files associated with this project. Each file will have the following association information:
- File type will be one of:
- Reference file: Obtained from an external source/database. When known, the obtained data and a link to the external source is included.
- Modified reference file: Obtained from an external source/database but modified for OpenPBTA use.
- PBTA data file: Pediatric Brain Tumor Atlas data that are processed upstream of the OpenPBTA project, e.g., the output of a somatic single nucleotide variant method. Links to the relevant D3B Center or Kids First workflow (and version where applicable) are included in Origin.
- Analysis file: Any file created by a script in
analyses/*.
- Origin
- For PBTA data files, a link the relevant D3B Center or Kids First workflow (and version where applicable).
- When applicable, a link to the specific script that produced (or modified, for Modified reference file types) the data.
- File description
- A brief one sentence description of what the file contains (e.g., bed files contain coordinates for features XYZ).
| File name | File Type | Origin | File Description |
|---|---|---|---|
fusion_summary_embryonal_foi.tsv |
Analysis file | analysis/fusion-summary |
Summary file for presence of embryonal tumor fusions of interest |
fusion_summary_ependymoma_foi.tsv |
Analysis file | analysis/fusion-summary |
Summary file for presence of ependymal tumor fusions of interest |
fusion_summary_ewings_foi.tsv |
Analysis file | analysis/fusion-summary |
Summary file for presence of Ewing's sarcoma fusions of interest |
gencode.v27.primary_assembly.annotation.gtf.gz |
Reference file | GENCODE v27 | hg38 gene annotation on primary assembly (reference chromosomes and scaffolds) |
GRCh38.primary_assembly.genome.fa.gz |
Reference Genome file | GENCODE v27 | hg38 primary assembly genome sequence FASTA file |
independent-specimens.wgs.primary-plus.tsv |
Analysis file | analyses/independent-samples |
Independent specimens list for WGS sample, primary + non-primary when no primary sample is available |
independent-specimens.wgs.primary.tsv |
Analysis file | analyses/independent-samples |
Independent specimens list for WGS samples, primary only |
independent-specimens.wgswxs.primary-plus.tsv |
Analysis file | analyses/independent-samples |
Independent specimens list for WGS and WXS samples, primary + non-primary when no primary sample is available |
independent-specimens.wgswxs.primary.tsv |
Analysis file | analyses/independent-samples |
Independent specimens list for WGS and WXS samples, primary only |
intersect_cds_lancet.bed |
Analysis file | analyses/snv-callers |
Intersection of gencode.v27.primary_assembly.annotation.gtf.gz CDS with WXS 100bp padded BED regions and Lancet's WXS regions |
intersect_cds_lancet_strelka_mutect_WGS.bed |
Analysis file | analyses/snv-callers |
Intersection of gencode.v27.primary_assembly.annotation.gtf.gz CDS with Lancet, Strelka2, Mutect2 regions |
intersect_strelka_mutect_WGS.bed |
Analysis file | analyses/snv-callers |
Intersection of gencode.v27.primary_assembly.annotation.gtf.gz CDS with Strelka2 and Mutect2 regions called |
pbta-cnv-cnvkit-gistic.zip |
PBTA data file | Workflow | Somatic CNV - GISTIC 2.0 output using pbta-cnv-cnvkit.seg file input (WGS samples only) |
pbta-cnv-consensus-gistic.zip |
Analysis file | Workflow | Somatic CNV - GISTIC 2.0 output using pbta-cnv-consensus.seg file input (WGS samples only) |
pbta-cnv-cnvkit.seg.gz |
PBTA data file | Copy number variant calling; Workflow | Somatic Copy Number Variant - CNVkit SEG file (WGS samples only) |
pbta-cnv-consensus.seg.gz |
Analysis file | CNV consensus calls | Somatic Copy Number Variant - CNVkit SEG file (WGS samples only) |
pbta-cnv-controlfreec.tsv.gz |
PBTA data file | Copy number variant calling; Workflow | Somatic Copy Number Variant - TSV file that is a merge of ControlFreeC *_CNVs files (WGS samples only) |
consensus_seg_annotated_cn_autosomes.tsv.gz |
Analysis file | Focal CNV consensus calls | TSV file containing genes with copy number changes per biospecimen; autosomes only |
consensus_seg_annotated_cn_x_and_y.tsv.gz |
Analysis file | Focal CNV consensus calls | TSV file containing genes with copy number changes per biospecimen; sex chromosomes only |
pbta-fusion-arriba.tsv.gz |
PBTA data file | Gene fusion detection; Workflow | Fusion - Arriba TSV, annotated with FusionAnnotator |
pbta-fusion-putative-oncogenic.tsv |
Analysis file | analyses/fusion_filtering |
Filtered and prioritized fusions |
pbta-fusion-recurrently-fused-genes-byhistology.tsv |
Analysis file | analysis/fusion-filtering |
Recurrently-fused genes tabulated by broad histology |
pbta-fusion-recurrently-fused-genes-bysample.tsv |
Analysis file | analysis/fusion-filtering |
Binary matrix that denotes the presence or absence of a recurrently fused gene in an individual RNA-seq specimen |
pbta-fusion-starfusion.tsv.gz |
PBTA data file | Gene fusion detection; Workflow | Fusion - STARFusion TSV |
pbta-gene-counts-rsem-expected_count.polya.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM expected counts for poly-A samples (gene-level) |
pbta-gene-counts-rsem-expected_count.stranded.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM expected counts for stranded samples (gene-level) |
pbta-gene-expression-kallisto.polya.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - kallisto TPM for poly-A samples (transcript-level) |
pbta-gene-expression-kallisto.stranded.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - kallisto TPM for stranded samples (transcript-level) |
pbta-gene-expression-rsem-fpkm-collapsed.polya.rds |
Analysis file | analyses/collapse-rnaseq |
Gene expression - RSEM FPKM for poly-A samples collapsed to gene symbol (gene-level) |
pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds |
Analysis file | analyses/collapse-rnaseq |
Gene expression - RSEM FPKM for stranded samples collapsed to gene symbol (gene-level) |
pbta-gene-expression-rsem-fpkm.polya.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM FPKM for poly-A samples (gene-level) |
pbta-gene-expression-rsem-fpkm.stranded.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM FPKM for stranded samples (gene-level) |
pbta-gene-expression-rsem-tpm.polya.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM TPM for poly-A samples (gene-level) |
pbta-gene-expression-rsem-tpm.stranded.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM TPM for stranded samples (gene-level) |
pbta-histologies.tsv |
PBTA data file | Clinical data harmonization | Harmonized clinical metadata file (see data dictionary here) |
pbta-isoform-counts-rsem-expected_count.polya.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM expected counts for poly-A samples (transcript-level) |
pbta-isoform-counts-rsem-expected_count.stranded.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM expected counts for stranded samples (transcript-level) |
pbta-isoform-expression-rsem-tpm.polya.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM TPM for poly-A samples (transcript-level) |
pbta-isoform-expression-rsem-tpm.stranded.rds |
PBTA data file | Gene expression abundance estimation; Workflow | Gene expression - RSEM TPM for stranded samples (transcript-level) |
pbta-mend-qc-manifest.tsv |
PBTA data file | MendQC analysis placeholder; Workflow |
File to map MendQC output to biospecimen IDs |
pbta-mend-qc-results.tar.gz |
PBTA data file | MendQC analysis placeholder; Workflow |
MendQC output files |
pbta-snv-consensus-mutation.maf.tsv.gz |
Analysis file | analyses/snv-callers |
Consensus calls for SNVs and small indels; columns in the included file are derived from the Strelka2. |
pbta-snv-consensus-mutation-tmb-all.tsv |
Analysis file | analyses/snv-callers |
Tumor mutation burden statistics calculated from Strelka2 and Mutect2 SNV consensus, and the intersection of Strelka2 and Mutect2 BED windows sizes. |
pbta-snv-consensus-mutation-tmb-coding.tsv |
Analysis file | analyses/snv-callers |
Coding only tumor mutation burden statistics calculated from the number of coding sequence Strelka2, Mutect2, and Lancet consensus SNVs and size of the intersection of all three callers' BED windows and the Gencode v27 coding sequences. |
pbta-snv-lancet.vep.maf.gz |
PBTA data file | Somatic mutation calling; Workflow | Somatic SNV - Lancet annotated MAF file |
pbta-snv-mutect2.vep.maf.gz |
PBTA data file | Somatic mutation calling; Workflow | Somatic SNV - Mutect2 annotated MAF file |
pbta-snv-strelka2.vep.maf.gz |
PBTA data file | Somatic mutation calling; Workflow | Somatic SNV - Strelka2 annotated MAF file |
pbta-snv-vardict.vep.maf.gz |
PBTA data file | Somatic mutation calling; Workflow | Somatic SNV - VarDict annotated MAF file |
pbta-star-log-final.tar.gz |
PBTA data file | Gene expression abundance estimation; Workflow | STAR log final output files |
pbta-star-log-manifest.tsv |
PBTA data file | Gene expression abundance estimation; Workflow | File to map STAR output to biospecimen IDs |
pbta-sv-manta.tsv.gz |
PBTA data file | Structural variant calling; Workflow | Somatic Structural Variant - Manta output, annotated with AnnotSV (WGS samples only) |
pbta-tcga-manifest.tsv |
PBTA data file | Somatic mutation calling | Manifest of tumor/normal BAMs used for SNV calling, Tumor_Sample_Barcodes, and histologies |
pbta-tcga-snv-lancet.vep.maf.gz |
PBTA/TCGA data file | Somatic mutation calling; Workflow | Somatic SNV - Lancet annotated MAF file |
pbta-tcga-snv-mutect2.vep.maf.gz |
PBTA data file | Somatic mutation calling; Workflow | Somatic SNV - Mutect2 annotated MAF file |
pbta-tcga-snv-strelka2.vep.maf.gz |
PBTA data file | Somatic mutation calling; Workflow | Somatic SNV - Strelka2 annotated MAF file |
StrexomeLite_hg38_liftover_100bp_padded.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 targeted panel regions used for all variant callers, each region padded by 100 bp |
StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed |
Target/Baits File | SNV and INDEL calling | hg38 targeted DNA panel bait capture regions provided by the kit manufacturer |
WGS.hg38.lancet.300bp_padded.bed |
Reference Target/Baits File | SNV and INDEL calling | WGS.hg38.lancet.unpadded.bed file with each region padded by 300 bp |
WGS.hg38.lancet.unpadded.bed |
Reference Regions File | SNV and INDEL calling | hg38 WGS regions created using UTR, exome, and start/stop codon features of the GENCODE 31 reference, augmented with PASS variant calls from Strelka2 and Mutect2 |
WGS.hg38.mutect2.vardict.unpadded.bed |
Reference Regions File | SNV and INDEL calling | hg38 BROAD Institute interval calling list (restricted to Chr1-22,X,Y,M and non-N regions) used for Mutect2 and VarDict variant callers |
WGS.hg38.strelka2.unpadded.bed |
Reference Regions File | SNV and INDEL calling | hg38 BROAD Institute interval calling list (restricted to Chr1-22,X,Y,M) used for Strelka2 variant caller |
WGS.hg38.vardict.100bp_padded.bed |
Reference Regions File | SNV and INDEL calling | WGS.hg38.mutect2.vardict.unpadded.bed with each region padded by 100 bp used for VarDict variant caller |
WXS.hg38.100bp_padded.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 WXS regions provided by the kit manufacturer used for Strelka2, Mutect2, and VarDict variant callers with each region padded by 100 bp |
WXS.hg38.lancet.400bp_padded.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 WXS regions provided by the kit manufacturer used for Lancet variant callers with each region padded by 400 bp |
intersected_whole_exome_agilent_designed_120_AND_tcga_6k_genes.Gh38.bed |
Reference Target/Baits File | SNV and INDEL calling | Generated using bedtools intersect from tcga_6k_genes.targetIntervals.Gh38.bed and whole_exome_agilent_designed_120.targetIntervals.Gh38.bed |
intersected_whole_exome_agilent_plus_tcga_6k_AND_tcga_6k_genes.Gh38.bed |
Reference Target/Baits File | SNV and INDEL calling | Generated using bedtools intersect from tcga_6k_genes.targetIntervals.Gh38.bed and whole_exome_agilent_plus_tcga_6k.targetIntervals.Gh38.bed |
tcga_6k_genes.targetIntervals.Gh38.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 version of tcga_6k_genes.targetIntervals.bed. Generated using CrossMap and bedtools sort and merge. Script in TCGA-capture-kit-analyses |
tcga_6k_genes.targetIntervals.bed |
Reference Target/Baits File | SNV and INDEL calling | hg19 WXS target capture regions downloaded from GDC website API endpoint. Script to retreive file described in TCGA-capture-kit-analyses |
whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.Gh38.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 version of whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.bed. Generated using CrossMap and bedtools sort and merge. Script in TCGA-capture-kit-analyses |
whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.bed |
Reference Target/Baits File | SNV and INDEL calling | hg19 WXS target capture regions downloaded from GDC website API endpoint. Script to retreive file described in TCGA-capture-kit-analyses |
whole_exome_agilent_designed_120.targetIntervals.Gh38.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 version of whole_exome_agilent_designed_120.targetIntervals.bed. Generated using CrossMap and bedtools sort and merge. Script in TCGA-capture-kit-analyses |
whole_exome_agilent_designed_120.targetIntervals.bed |
Reference Target/Baits File | SNV and INDEL calling | hg19 WXS target capture regions downloaded from GDC website API endpoint. Script to retreive file described in TCGA-capture-kit-analyses |
whole_exome_agilent_plus_tcga_6k.targetIntervals.Gh38.bed |
Reference Target/Baits File | SNV and INDEL calling | hg38 version of whole_exome_agilent_plus_tcga_6k.targetIntervals.bed. Generated using CrossMap and bedtools sort and merge. Script in TCGA-capture-kit-analyses |
whole_exome_agilent_plus_tcga_6k.targetIntervals.bed |
Reference Target/Baits File | SNV and INDEL calling | hg19 WXS target capture regions downloaded from GDC website API endpoint. Script to retreive file described in TCGA-capture-kit-analyses |