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DNAscope: High accuracy small variant calling using machine learning

View ORCID ProfileDonald Freed, Renke Pan, Haodong Chen, Zhipan Li, Jinnan Hu, Rafael Aldana
doi: https://doi.org/10.1101/2022.05.20.492556
Donald Freed
Sentieon Inc., San Jose, CA
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  • ORCID record for Donald Freed
  • For correspondence: don.freed@sentieon.com
Renke Pan
Sentieon Inc., San Jose, CA
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Haodong Chen
Sentieon Inc., San Jose, CA
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Zhipan Li
Sentieon Inc., San Jose, CA
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Jinnan Hu
Sentieon Inc., San Jose, CA
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Rafael Aldana
Sentieon Inc., San Jose, CA
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Abstract

We present DNAscope, an accurate and efficient germline small-variant caller. DNAscope combines the robust and well-established preprocessing and assembly mathematics of the GATK’s HaplotypeCaller with a machine-learned genotyping model. Benchmarks of DNAscope and DNAseq (Sentieon’s GATK-matching germline variant calling pipeline) demonstrate that DNAscope achieves superior SNP and insertion/deletion accuracy with reduced computational cost.

Competing Interest Statement

D.F., H.C., Z.L., J.H. and R.A. are current employees of Sentieon, Inc., and hold stock options as part of the standard compensation package. R.P. is former employee of Sentieon.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 22, 2022.
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DNAscope: High accuracy small variant calling using machine learning
Donald Freed, Renke Pan, Haodong Chen, Zhipan Li, Jinnan Hu, Rafael Aldana
bioRxiv 2022.05.20.492556; doi: https://doi.org/10.1101/2022.05.20.492556
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DNAscope: High accuracy small variant calling using machine learning
Donald Freed, Renke Pan, Haodong Chen, Zhipan Li, Jinnan Hu, Rafael Aldana
bioRxiv 2022.05.20.492556; doi: https://doi.org/10.1101/2022.05.20.492556

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