Strelka2: fast and accurate calling of germline and somatic variants

Nature Methods
Sangtae KimChristopher T Saunders

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.

References

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Citations

May 18, 2019·Bioinformatics·Daniel TelloJorge Duitama
Apr 17, 2019·Genes·Tatiana Maroilley, Maja Tarailo-Graovac
May 2, 2019·Genome Medicine·Markus W LöfflerHans-Georg Rammensee
Jul 10, 2019·PloS One·Azza E AhmedLiudmila S Mainzer
Mar 13, 2020·Stem Cells Translational Medicine·Annegien T KenterJoost H Gribnau
Apr 1, 2020·International Journal of Molecular Sciences·Sylvan M CasparGabor Matyas
Aug 31, 2019·PLoS Computational Biology·Laxmi ParidaTorsten Haferlach
Oct 9, 2019·Scientific Reports·Deepika KanojiaPhillip Koeffler
Jun 9, 2020·EMBO Molecular Medicine·Silvia BenvenutiPaolo M Comoglio
Jun 21, 2019·Nature Protocols·James BlackburnTim R Mercer
Jun 27, 2020·Blood Advances·Christopher K RushtonRyan D Morin
Aug 25, 2019·Molecular Cancer·Miao PengZhaoyang Zeng
Oct 9, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Andrew M GrossRyan J Taft
Jan 8, 2020·Nature Biotechnology·Yanmei DouPeter J Park
Jun 20, 2020·Nature Communications·Bin ZhuMaria Teresa Landi
Jun 26, 2020·Nature·Sarah J AitkenMartin S Taylor
Jul 8, 2020·BMC Medical Genomics·Louise de Schaetzen van BrienenKathleen Marchal
Jul 3, 2020·PeerJ·Robert Edgar
Jul 17, 2020·Nature·Gary MiddletonLucinda Billingham
Mar 25, 2019·Nature Communications·Ira W DevesonTim R Mercer

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Datasets Mentioned

BETA
NA12878
SRP142632
EGAS00001001539

Methods Mentioned

BETA
genotyping
RNA-seq

Software Mentioned

Strelka2
Platypus
mathop
GATK4
nextgen
FreeBayes
VarDict
TIGRA
Scalpel
MuTect2

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