2 posts tagged with "structural-variants"

Structural variants (SVs) are large-scale genomic alterations (≥50 bp) including deletions, duplications, inversions, and translocations. While short-read sequencing has revolutionized SNP and small indel detection, structural variant calling remains a significant challenge. This blog explores SV calling tools for germline samples with 30X short reads, benchmarks five popular callers (Manta, TIDDIT, Delly, Smoove, CNVnator), and reveals fundamental limitations in both detection tools and evaluation methods. The results show that even the best-performing tool (Manta) achieves only 36.8% precision when evaluated with Truvari, while alternative evaluation methods from 2019 report >80% precision - highlighting the complexity and ambiguity inherent in SV analysis.

Structural variants (SVs) — deletions, insertions, duplications, inversions, and translocations — are large genomic alterations (typically ≥50 bp) that play a major role in disease but are much harder to detect than SNPs or small indels. In this post, we benchmark Manta, the SV caller integrated in nf-core/sarek, against the GIAB HG002 truth set using Truvari, and explore why short-read SV calling remains a fundamentally difficult problem.