VALOR2: characterization of large-scale structural variants using linked-reads

Genome Biol. 2020 Mar 19;21(1):72. doi: 10.1186/s13059-020-01975-8.


Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, for example, inversions and translocations, is a particularly challenging task. Furthermore, there are very few algorithms to predict the insertion locus of large interspersed segmental duplications and characterize translocations. Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data. We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.

Keywords: Linked-reads; Structural variation; WGS.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Chromosome Duplication
  • Chromosome Inversion
  • Cluster Analysis
  • Genomic Structural Variation*
  • Humans
  • Sequence Deletion
  • Software*
  • Translocation, Genetic