Structural variants

Manta

Structural variants are changes from about 50 base pairs upward: missing or duplicated segments, inversions or translocations. They can affect entire genes and are demanding to detect with short-read sequencing. Genome calls them from the alignments.

Why they are hard to find

A short read of about a hundred bases cannot span a large rearrangement. Callers therefore infer indirectly from signals: pairs that map too far apart, reads split at a breakpoint, or regions with conspicuously high or low coverage. Repetitive regions further complicate unambiguous assignment.

How Genome analyses

Genome uses Manta. The caller combines paired and split-read evidence and locally re-assembles breakpoints to report structural variants efficiently. Genome carries the findings as technical candidates with evidence; assessment and confirmation remain a qualified step.

What Genome measures. Candidate structural variants (deletions, duplications, insertions, inversions, breakends) with position, type and supporting evidence from the read pattern.

Related topics

Repeat expansionsLp(a) and KIV-2

Sources

  1. 1Chen et al., 2016 Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32:1220–1222. doi.org/10.1093/bioinformatics/btv710
  2. 2Mahmoud et al., 2019 Structural variant calling: the long and the short of it. Genome Biology 20:246. doi.org/10.1186/s13059-019-1828-7