Strelka2: fast and accurate calling of germline and somatic variants

Nat Methods. 2018 Aug;15(8):591-594. doi: 10.1038/s41592-018-0051-x. Epub 2018 Jul 16.


We describe Strelka2 ( ), 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.

MeSH terms

  • Databases, Genetic / statistics & numerical data
  • Genetic Variation*
  • Germ-Line Mutation*
  • Haplotypes
  • High-Throughput Nucleotide Sequencing / statistics & numerical data
  • Humans
  • INDEL Mutation
  • Models, Genetic
  • Neoplasms / genetics
  • Software*
  • Whole Genome Sequencing / statistics & numerical data