Strelka2: fast and accurate calling of germline and somatic variants

• DOI: 10.1038/s41592-018-0051-x
• Publication Date: 2018-07-11T14:32:21Z
• Authors: Sangtae Kim; Konrad Scheffler; Aaron L. Halpern; Mitchell A. Bekri...; Eunho Noh; Morten Källberg; Xiaoyu Chen; Yeonbin Kim; Doruk Beyter; Peter Krusche; Christopher T. Sa...
• Keywords: 0301 basic medicine; Models, Genetic; Whole Genome Sequencing; Genetic Variation; High-Throughput Nucleotide Sequencing; 03 medical and health sciences; Haplotypes; INDEL Mutation; Neoplasms; Databases, Genetic; Humans; Germ-Line Mutation; Software

We describe Strelka2 ( https://github.com/Illumina/strelka ), an open-source small-variant-calling method for research and clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model-based estimation of insertion/deletion error parameters from each sample, an efficient tiered haplotype-modeling strategy, and a normal sample contamination model to improve liquid tumor analysis. For both germline and somatic calling, Strelka2 substantially outperformed the current leading tools in terms of both variant-calling accuracy and computing cost.