Abstract

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 incorporates improvements for fast and accurate calling of somatic and germline single-nucleotide variants and indels.

Keywords

GermlineSomatic cellComputational biologyGermline mutationHaplotypeOpen sourceComputer scienceBiologySample (material)GeneticsMutationGenotypeGeneSoftware

MeSH Terms

DatabasesGeneticGenetic VariationGerm-Line MutationHaplotypesHigh-Throughput Nucleotide SequencingHumansINDEL MutationModelsGeneticNeoplasmsSoftwareWhole Genome Sequencing

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Publication Info

Year
2018
Type
article
Volume
15
Issue
8
Pages
591-594
Citations
1621
Access
Closed

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Cite This

Sangtae Kim, Konrad Scheffler, Aaron L. Halpern et al. (2018). Strelka2: fast and accurate calling of germline and somatic variants. Nature Methods , 15 (8) , 591-594. https://doi.org/10.1038/s41592-018-0051-x

Identifiers

DOI
10.1038/s41592-018-0051-x
PMID
30013048

Data Quality

Data completeness: 86%