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[Preprint]. 2023 Apr 5:2023.01.12.523790. Originally published 2023 Jan 15. [Version 2] doi: 10.1101/2023.01.12.523790

Figure 2. Small variant calling performance evaluation.

Figure 2.

(Left panels) Number of false positive (light bars) and false negative (dark bars) calls made by PEPPER-Margin-DeepVariant (PMDV) using ONT reads and DeepVariant using Illumina reads. Statistics computed against the Genome in a Bottle v4.2.1 benchmark for HG002; for other cell lines (HG00733, HG02723) calls generated by DeepVariant with HiFi reads are used. Whole genome SNP counts are stratified by mappability in (A) and local context in (B); INDEL counts by local context in (C). (Right panels) Number of true positive variant calls stratified by different genomic intervals. F1-score is reported on top of each bar.