Fig. 1: Pipeline and quality control for identification of 3′-UTR variants in TCGA STAD cohort. | Nature Communications

Fig. 1: Pipeline and quality control for identification of 3′-UTR variants in TCGA STAD cohort.

From: Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci

Fig. 1

A Flowchart showing the variant-calling pipeline used for the analysis of TCGA STAD raw RNAseq data. B Distribution of the relative position of single nucleotide variant calls along the 3′-UTR as identified by analysis of TCGA WES, RNAseq and WGS data. C Number of RNAseq-derived somatic 3′-UTR single nucleotide variants per sample, grouped by “Mutation Rate Category” as defined by TCGA WES variant-calling data. D Overlap between transcriptome-wide variant calls in the analysis of RNAseq data with GATK and Strelka2 (GATK = 5,431,118, Strelka2 = 10,175,223, Overlap = 4,692,062). Figure data are provided in the Source Data file.

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