Table 1.
Overview of SV detection methods and the types of SVs identified by different tools.
Fig 1.
SV detection workflow starts with benchmark set collection from GIAB and HGSVC2, followed by sequence alignment using BWA-MEM to produce BAM files. These BAM files are then processed by various SV callers (DRAGEN, Manta, DELLY, LUMPY, GRIDSS, SvABA) to generate VCF files, which are subsequently used for performance assessment, including single tool and combination strategies, based on recall, precision, and F1 score.
Fig 2.
The SVs detected by six SV callers.
(A) SVs of sizes ≥ 50 bp and CTX detected by individual SV callers in samples, HG002, HG00514, HG00733, and NA19240. (B) Length distribution of different variants for all samples detected by individual SV callers. The maximum, minimum, and median are based on the integrated values from all sample sets. DEL: deletion, INS: insertion, DUP: duplication, INV: inversion, and CTX: complex translocation.
Fig 3.
The distribution of SVs in truth sets and the performance of individual algorithms.
(A) The distribution of SVs size and types in truth sets. (B) The comparison of False negative (FN) and False positive (FP) numbers among individual algorithms. (C) The precision, recall, and F1 score of each individual algorithm in detecting “DELs” and “INSs” with the size ≥ 50 bp. DEL: deletion, INS: insertion.
Table 2.
Performance of single algorithm in detecting DELs and INSs.
Fig 4.
Concordance of neighbor SVs detected by member callers in different combination strategies.
(A) The agreement among three SV detection tools (Manta, DELLY, and GRIDSS). (B) The agreement among five SV detection tools (Manta, DELLY, GRIDSS, LUMPY, and SvABA).
Fig 5.
Distribution and performance of combination strategies.
(A) The distribution of SVs in different combination strategies. (B) The comparison of False negative (FN) and False positive (FP) numbers among individual algorithms. (C) The precision, recall, and F1 score of combination strategies in the detection of DELs and INSs. DEL: deletion, INS: insertions, DUP: duplication, INV: inversion.
Table 3.
Performance of different combination strategies in detecting DELs and INSs.
Fig 6.
Combination performance of each single caller and combination strategy in detecting DELs and INSs.
The maximum, minimum, and macro average of recall, precision, and F1 score are based on the integrated values from all sample sets.
Table 4.
Combined performance of single caller and different combination strategies in detecting DELs and INSs.