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Strelka2: fast and accurate calling of germline and somatic variants.

Sangtae KimKonrad SchefflerAaron L HalpernMitchell A BekritskyEunho NohMorten KällbergXiaoyu ChenYeonbin KimDoruk BeyterPeter KruscheChristopher T Saunders
Published in: Nature methods (2018)
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.
Keyphrases
  • copy number
  • dna repair
  • risk assessment
  • high resolution
  • dna damage
  • drinking water
  • genome wide
  • single cell
  • oxidative stress
  • mass spectrometry
  • human health
  • heavy metals