: We describe Manta, a method to discover structural variants and indels from 
next generation sequencing data. Manta is optimized for rapid germline and 
somatic analysis, calling structural variants, medium-sized indels and large 
insertions on standard compute hardware in less than a tenth of the time that 
comparable methods require to identify only subsets of these variant types: for 
example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta 
can discover and score variants based on supporting paired and split-read 
evidence, with scoring models optimized for germline analysis of diploid 
individuals and somatic analysis of tumor-normal sample pairs. Call quality is 
similar to or better than comparable methods, as determined by pedigree 
consistency of germline calls and comparison of somatic calls to COSMIC database 
variants. Manta consistently assembles a higher fraction of its calls to 
base-pair resolution, allowing for improved downstream annotation and analysis 
of clinical significance. We provide Manta as a community resource to facilitate 
practical and routine structural variant analysis in clinical and research 
sequencing scenarios.
AVAILABILITY AND IMPLEMENTATION: Manta is released under the open-source GPLv3 
license. Source code, documentation and Linux binaries are available from 
https://github.com/Illumina/manta.
CONTACT: csaunders@illumina.com
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.