Somatic structural variation discovery on cancer pangenome graphs

JANUS discovers somatic structural variants in personal pangenome graphs, achieving a mean F1 of 0.887 across five CASTLE tumor-normal pairs, leading the 18-caller consensus.

• Why it matters: Somatic SV detection is hindered by low variant allele frequencies and by computational cost and reference bias from aligning whole-genome reads to a single linear reference.
• What they did: JANUS builds a colored de Bruijn-like graph of locally consistent parsing cores from matched normal and tumor PacBio HiFi reads, then finds tumor-only traversals without prior alignment.
• The result: It widens its lead under low signal (F1 0.489 vs 0.362 at 5x; 0.683 vs 0.520 at 20% purity) and analyzes a pair in ~11 minutes with 16 threads (~24x faster than alignment).

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