Add CNVkit theta2 seg file to OPC v16

[jharenza]

Which new datasets are being added with this release?

What is the sample breakdown (number of WGS, WXS, RNA-Seq, Panel, Methylation, other)?

What module(s) generated any new files to include in the release? Has that module been added to the analysis/README.md, and to CI?

Are you aware of any modules impacted by the file(s) change(s)? Describe if the file name is changed.

What data file(s) are added/updated/removed in this release?

[Pre-release files]

• histologies-base.tsv
• cnv-cnvkit.seg.gz
• cnvkit_with_status.tsv
• cnv-controlfreec.tsv.gz
• cnv-consensus-gistic.zip
• cnv-consensus.seg.gz
• consensus_seg_with_status.tsv
• consensus_wgs_plus_cnvkit_wxs.tsv.gz
• consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
• consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
• fusion-arriba.tsv.gz
• fusion-dgd.tsv.gz
• fusion-putative-oncogenic.tsv
• fusion-starfusion.tsv.gz
• fusion_summary_embryonal_foi.tsv
• fusion_summary_ependymoma_foi.tsv
• fusion_summary_ewings_foi.tsv
• fusion_summary_lgat_foi.tsv
• snv-consensus-plus-hotspots.maf.tsv.gz
• snv-dgd.maf.tsv.gz
• sv-manta.tsv.gz
• snv-mutation-tmb-all.tsv
• snv-mutation-tmb-coding.tsv
• gene-expression-rsem-tpm-collapsed.rds
• gene-counts-rsem-expected_count-collapsed.rds
• tcga-gene-expression-rsem-tpm-collapsed.rds
• tcga-gene-counts-rsem-expected_count-collapsed.rds
• rna-isoform-expression-rsem-tpm.rds
• methyl-m-values.rds
• methyl-cn-values.rds
• methyl-beta-values.rds
• independent-specimens.rnaseq.primary-plus.pre-release.tsv
• independent-specimens.rnaseq.primary.pre-release.tsv
• independent-specimens.rnaseq.relapse.pre-release.tsv

[Commit files]

• histologies.tsv
• efo-mondo-map.tsv
• ensg-hugo-pmtl-mapping.tsv
• uberon-map-gtex-group.tsv
• uberon-map-gtex-subgroup.tsv
• independent-specimens.methyl.primary-plus.eachcohort.tsv
• independent-specimens.methyl.primary-plus.tsv
• independent-specimens.methyl.primary.eachcohort.tsv
• independent-specimens.methyl.primary.tsv
• independent-specimens.methyl.relapse.eachcohort.tsv
• independent-specimens.methyl.relapse.tsv
• independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
• independent-specimens.rnaseqpanel.primary-plus.tsv
• independent-specimens.rnaseqpanel.primary.eachcohort.tsv
• independent-specimens.rnaseqpanel.primary.tsv
• independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
• independent-specimens.rnaseqpanel.relapse.tsv
• independent-specimens.wgs.primary-plus.eachcohort.tsv
• independent-specimens.wgs.primary-plus.tsv
• independent-specimens.wgs.primary.eachcohort.tsv
• independent-specimens.wgs.primary.tsv
• independent-specimens.wgs.relapse.eachcohort.tsv
• independent-specimens.wgs.relapse.tsv
• independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
• independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
• independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
• independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
• independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
• independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
• independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
• independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
• independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
• independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
• independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
• independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv

[Bed files and sample mapping]

• biospecimen_id_to_bed_map.txt
• ashion_exome_v2_targets_hg38_padded100.bed
• hg38_strelka.bed
• intersect_cds_lancet_strelka_mutect_WGS.bed
• intersect_strelka_mutect_WGS.bed
• nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
• S0274956_Padded_HG38.merged.bed
• S02972011_Covered_hg38_100.bed
• S04380110_Regions_hg38_100.bed
• S07604715_100bp_Padded.bed
• SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
• StrexomeLite_hg38_liftover_100bp_padded.bed
• Strexome_targets_intersect_sorted_padded100.GRCh38.bed
• TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
• truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
• wgs_canonical_calling_regions.hg38.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
• xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

[File descriptions and notes]

• data-files-description.md
• release-notes.md

Any additional notes to add for discussion?

[jharenza]

now rokitalab#9