diff --git a/doc/release-notes.md b/doc/release-notes.md index ccc7f8c65a..2864f5ca8b 100644 --- a/doc/release-notes.md +++ b/doc/release-notes.md @@ -1,5 +1,139 @@ # release notes ## current release +### release-v19-20210423 +- release date: 2021-04-23 +- status: available +- changes: + - Remove per BS_JXF8A2A6 due to mis-identification per [#862](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/862) + - Updates: + - pbta-fusion-starfusion.tsv.gz + - pbta-fusion-arriba.tsv.gz + - pbta-gene-expression-rsem-fpkm.stranded.rds + - pbta-gene-counts-rsem-expected_count.stranded.rds + - pbta-gene-expression-rsem-tpm.stranded.rds + - pbta-gene-expression-kallisto.stranded.rds + - pbta-isoform-counts-rsem-expected_count.stranded.rds + - pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds + - pbta-isoform-expression-rsem-tpm.stranded.rds + - independent-specimens.rnaseq.primary-plus-stranded.tsv + - pbta-star-log-final.tar.gz + - pbta-star-log-manifest.tsv + - pbta-mend-qc-manifest.tsv + - pbta-mend-qc-results.tar.gz + - pbta-fusion-putative-oncogenic.tsv + - pbta-fusion-recurrently-fused-genes-byhistology.tsv + - pbta-fusion-recurrently-fused-genes-bysample.tsv + - independent-specimens.rnaseq.primary-plus-stranded.tsv + - fusion_summary_ewings_foi.tsv + - fusion_summary_lgat_foi.tsv + - fusion_summary_ependymoma_foi.tsv + - fusion_summary_embryonal_foi.tsv + - Add INDEL renormalization of MAF files per [#1024](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1024) + - Updates: + - pbta-snv-strelka2.vep.maf.gz + - pbta-snv-lancet.vep.maf.gz + - pbta-snv-vardict.vep.maf.gz + - pbta-snv-mutect2.vep.maf.gz + - pbta-tcga-snv-strelka2.vep.maf.gz + - pbta-tcga-snv-mutect2.vep.maf.gz + - pbta-tcga-snv-lancet.vep.maf.gz + - Update pbta-histologies.tsv: + - Add `PFS_days` to `pbta-histologies.tsv` file per [#963](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/963) + - Pull latest clinical data + - Rerun molecular subtyping modules to date + - Update PNOC003 `cohort` to "PNOC" for inclusion of later PNOC trial samples + - Update `CNS_region` from manual review per [#1025](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1025) + - Add `pbta-mb-pathology-subtypes.tsv` containing pathology report molecular subtypes for medulloblastoma to be used as a "truth" set for medulloblastoma classifier testing per [#746](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/746) +- folder structure: +``` +data +└── release-v19-20210423 + ├── 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 + ├── fusion_summary_lgat_foi.tsv + ├── independent-specimens.rnaseq.primary-plus-polya.tsv + ├── independent-specimens.rnaseq.primary-plus-stranded.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-histologies-base.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-scavenged-hotspots.maf.tsv.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 + ├── tcga-snv-consensus-snv.maf.tsv.gz + ├── tcga-snv-mutation-tmb-all.tsv + ├── tcga-snv-mutation-tmb-coding.tsv + ├── 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-v18-20201123 - release date: 2020-11-23 - status: available diff --git a/download-data.sh b/download-data.sh index fc021f177d..e86d08ac5f 100755 --- a/download-data.sh +++ b/download-data.sh @@ -4,8 +4,8 @@ set -o pipefail # Use the OpenPBTA bucket as the default. URL=${OPENPBTA_URL:-https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/data} -RELEASE=${OPENPBTA_RELEASE:-release-v18-20201123} -PREVIOUS=${OPENPBTA_RELEASE:-release-v17-20200908} +RELEASE=${OPENPBTA_RELEASE:-release-v19-20210423} +PREVIOUS=${OPENPBTA_RELEASE:-release-v18-20201123} # Remove old symlinks in data find data -type l -delete