Svtools: Population-scale analysis of structural variation

David E. Larson, Haley J. Abel, Colby Chiang, Abhijit Badve, Indraniel Das, James M. Eldred, Ryan M. Layer, Ira M. Hall

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Large-scale human genetics studies are now employing whole genome sequencing with the goal of conducting comprehensive trait mapping analyses of all forms of genome variation. However, methods for structural variation (SV) analysis have lagged far behind those for smaller scale variants, and there is an urgent need to develop more efficient tools that scale to the size of human populations. Here, we present a fast and highly scalable software toolkit (svtools) and cloud-based pipeline for assembling high quality SV maps - including deletions, duplications, mobile element insertions, inversions and other rearrangements - in many thousands of human genomes. We show that this pipeline achieves similar variant detection performance to established per-sample methods (e.g. LUMPY), while providing fast and affordable joint analysis at the scale of ≥100 000 genomes. These tools will help enable the next generation of human genetics studies.

Original languageEnglish
Pages (from-to)4782-4787
Number of pages6
Issue number22
StatePublished - Nov 1 2019


Dive into the research topics of 'Svtools: Population-scale analysis of structural variation'. Together they form a unique fingerprint.

Cite this