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Fig. 1 | Genome Biology

Fig. 1

From: Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Fig. 1

BAMSurgeon simulates SVs in genome sequences. Method for adding SVs to existing BAM alignments. a Overview of SV (e.g., deletion) spike-in: Starting with an original BAM (i), a region (ii) is selected where a deletion is desired. (iii) Contigs are assembled from reads in the selected region, and the contig is rearranged by deleting the middle. The amount of contig deleted is a user-definable parameter. Read coverage is generated over the contig using wgsim to match the number of reads per base in the original BAM. Since the deletion contig is shorter than the original, fewer reads will be required to achieve the equivalent coverage. (iv) Generated read pairs include discordant pairs (i.e., paired reads that do not align to the reference genome with the expected relative orientation and inner distance) spanning the deletion and clipped reads (i.e., reads that are only partially aligned to the reference). Reads mapping to the deleted region of the contig are not included in the final BAM. b, c To test the robustness of BAMSurgeon with respect to changes in (b) aligner and (c) cell line, we compared the ranks of CREST, Delly, Manta, and novoBreak on two new tumor-normal datasets: one with an alternative aligner, NovoAlign, and the other on an alternative cell line, HCC1954 BL. Callers were scored with f = 100 bp (Additional file 1: Figure S2b); Manta retained the top position, independent of aligner and cell line. d Summary of the three in silico (IS) tumors described here. Abbreviations: DEL, deletion; DUP, duplication; INV, inversion; INS, insertion

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