Gene

Biology

Chromatography

Open source

Somatic cell

Mutation

Computer science

Germline

Computational biology

Software

Genetics

Germline mutation

Genotype

Haplotype

Chemistry

Programming language

Sample (material)

Nature Methods

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.

Strelka2: fast and accurate calling of germline and somatic variants