Variant Calling (Part 8): Structural Variant Calling Short Read Benchmark
· 8 min read
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.