UpSet with cap S

content/08.supplemental.md

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 ![**OpenPBTA Project Workflow, Related to Figure 1.** Biospecimens and data were collected by CBTN and PNOC. Genomic sequencing and harmonization (orange boxes) were performed by the Kids First Data Resource Center (KFDRC). Analyses in the green boxes were performed by contributors of the OpenPBTA project. Output files are denoted in blue. Figure created with [BioRender.com](biorender.com).](https://raw.githubusercontent.com/AlexsLemonade/OpenPBTA-analysis/37ec62fdc2fd9ff157f2f2c10b69e9bb36673363/figures/pngs/figureS1.png?sanitize=true){#fig:S1 tag="S1" width="7in"}
 
-![**Validation of Consensus SNV calls and Tumor Mutation Burden, Related to Figures 2 and 3.** Correlation (A) and violin (B) plots of mutation variant allele frequencies (VAFs) comparing the variant callers (Lancet, Strelka2, Mutect2, and VarDict) used for PBTA samples. Upset plot (C) showing overlap of variant calls. Correlation (D) and violin (E) plots of mutation variant allele frequencies (VAFs) comparing the variant callers (Lancet, Strelka2, and Mutect2) used for TCGA samples. Upset plot (F) showing overlap of variant calls. Violin plots (G) showing VAFs for Lancet calls performed on WGS and WXS from the same tumor (N = 52 samples from 13 patients). Cumulative distribution TMB plots for PBTA (H) and TCGA (I) tumors using consensus SNV calls.](https://raw.githubusercontent.com/AlexsLemonade/OpenPBTA-analysis/37ec62fdc2fd9ff157f2f2c10b69e9bb36673363/figures/pngs/figureS2.png?sanitize=true){#fig:S2 tag="S2" width="7in"}
+![**Validation of Consensus SNV calls and Tumor Mutation Burden, Related to Figures 2 and 3.** Correlation (A) and violin (B) plots of mutation variant allele frequencies (VAFs) comparing the variant callers (Lancet, Strelka2, Mutect2, and VarDict) used for PBTA samples. UpSet plot (C) showing overlap of variant calls. Correlation (D) and violin (E) plots of mutation variant allele frequencies (VAFs) comparing the variant callers (Lancet, Strelka2, and Mutect2) used for TCGA samples. UpSet plot (F) showing overlap of variant calls. Violin plots (G) showing VAFs for Lancet calls performed on WGS and WXS from the same tumor (N = 52 samples from 13 patients). Cumulative distribution TMB plots for PBTA (H) and TCGA (I) tumors using consensus SNV calls.](https://raw.githubusercontent.com/AlexsLemonade/OpenPBTA-analysis/37ec62fdc2fd9ff157f2f2c10b69e9bb36673363/figures/pngs/figureS2.png?sanitize=true){#fig:S2 tag="S2" width="7in"}
 
 ![**Genomic instability of pediatric brain tumors, Related to Figures 2 and 3.** (A) Violin plots of tumor purity by cancer group. Dots represent the group median. (B) Oncoprint of canonical somatic gene mutations, CNVs, fusions, and TMB (top bar plot) for the top mutated genes across rare CNS tumors: desmoplastic infantile astrocytoma and ganglioglioma (N = 2), germinoma (N = 4), glial-neuronal NOS (N = 8), metastatic secondary tumors (N = 2), neurocytoma (N = 2), pineoblastoma (N = 4), Rosai-Dorfman disease (N = 2), and sarcomas (N = 4). Patient sex (`Germline sex estimate`) and tumor histology (`Cancer Group`) are displayed as annotations at the bottom of each plot. Multiple CNVs are denoted as a complex event. N denotes the number of unique tumors with one tumor per patient used. (C) Genome-wide plot of CNV alterations by broad histology. Each row represents one sample. Box and whisker plots of number of CNV breaks (D) or SV breaks (E) by number of chromothripsis regions. Box plot represents 5% (lower whisker), 25% (lower box), 50% (median), 75% (upper box), and 95% (upper whisker) quantiles.](https://raw.githubusercontent.com/AlexsLemonade/OpenPBTA-analysis/37ec62fdc2fd9ff157f2f2c10b69e9bb36673363/figures/pngs/figureS3.png?sanitize=true){#fig:S3 tag="S3" width="7in"}