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

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

Author information

1
Illumina, Inc., San Diego, CA, USA.
2
Illumina Cambridge Ltd, Essex, UK.
3
Seven Bridges Genomics, London, UK.
4
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
5
deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
6
Illumina, Inc., San Diego, CA, USA. csaunders@illumina.com.

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.

PMID:
30013048
DOI:
10.1038/s41592-018-0051-x
[Indexed for MEDLINE]

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