Fig. 4: Orthogonal SV validation with overlapping calls among different tools and with the new complete human genome reference T2T-CHM13. | Nature Communications

Fig. 4: Orthogonal SV validation with overlapping calls among different tools and with the new complete human genome reference T2T-CHM13.

From: Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data

Fig. 4

a, b Overlapping TP deletion and insertion SVs supported by read alignment-based and assembly-based tools. c, d Overlapping FP deletion and insertion SVs supported by read alignment-based and assembly-based tools. e, f Overlapping FN deletion and insertion SVs supported by read alignment-based and assembly-based tools. The top panels show results by using high-confidence benchmark SVs from GIAB (with constraints), and the bottom panels show results by using all benchmark SVs (without constraints). The height of each bar represents the total SVs discovered by a tool. Color gradient in the bar specifies a range of supporting tools for SVs. Dark colors represent a high number of supporting tools, while light colors represent a low number of supporting tools. g Percentage of FP deletions and insertions supported by T2T-CHM13 for each SV caller. h Size distribution of total FPs (without constraints) and FPs supported by T2T-CHM13. i Percentage of FP deletions and insertions supported by Verkko assembly for each SV caller. Source data are provided as a Source Data file.

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