Figure 1 from Improving Long-Read Somatic Structural Variant Calling with Pangenome and <i>De Novo</i> Personal Genome Assembly

Minisv starts from the existing somatic SV call set. Step (1) Extract reads from somatic SVs in the tumor from the call set; (2) realign SV-containing reads to GRCh38, normal self-assembly (if available), and/or pangenome and extract candidate SVs from the realignment in the read coordinate; (3) compare the candidate SVs resulting from the alignment against multiple genomes; and (4) for each SV call set, extract supporting reads and filter a read if its alignment to the self-assembly and/or pangenome does not contain the SV.

Given multiple SV callers, minisv can generate a union somatic call set. Gray boxes denote the reference genome such as GRCh38; cyan boxes denote contigs from self-assembly; short red bars indicate potential somatic SVs; thin blue lines correspond to reads from the tumor aligned to the contigs of different reference genomes; thin orange lines correspond to reads from the normal control; and large brown circles indicate pangenome variant nodes that vary across individuals.</p>