SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy

Katherine I. Kendig, Saurabh Baheti, Matthew A. Bockol, Travis M. Drucker, Steven Hart, Jacob R. Heldenbrand, Mikel Hernaez, Matthew E. Hudson, Michael T. Kalmbach, Eric W Klee, Nathan R. Mattson, Christian A. Ross, Morgan Taschuk, Eric D Wieben, Mathieu Wiepert, Derek E. Wildman, Liudmila S. Mainzer

Research output: Contribution to journalArticle

Abstract

As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The Genome Analysis Toolkit (GATK), maintained by the Broad Institute, is currently the widely accepted standard for variant calling software. However, alternative solutions may provide faster variant calling without sacrificing accuracy. One such alternative is Sentieon DNASeq, a toolkit analogous to GATK but built on a highly optimized backend. We conducted an independent evaluation of the DNASeq single-sample variant calling pipeline in comparison to that of GATK. Our results support the near-identical accuracy of the two software packages, showcase optimal scalability and great speed from Sentieon, and describe computational performance considerations for the deployment of DNASeq.

Original languageEnglish (US)
Article number736
JournalFrontiers in Genetics
Volume10
Issue numberJUL
DOIs
StatePublished - Jan 1 2019

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Keywords

  • Benchmarking
  • DNASeq
  • GATK
  • Sentieon
  • Variant calling

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)

Cite this

Kendig, K. I., Baheti, S., Bockol, M. A., Drucker, T. M., Hart, S., Heldenbrand, J. R., ... Mainzer, L. S. (2019). SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy. Frontiers in Genetics, 10(JUL), [736]. https://doi.org/10.3389/fgene.2019.00736

SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy. / Kendig, Katherine I.; Baheti, Saurabh; Bockol, Matthew A.; Drucker, Travis M.; Hart, Steven; Heldenbrand, Jacob R.; Hernaez, Mikel; Hudson, Matthew E.; Kalmbach, Michael T.; Klee, Eric W; Mattson, Nathan R.; Ross, Christian A.; Taschuk, Morgan; Wieben, Eric D; Wiepert, Mathieu; Wildman, Derek E.; Mainzer, Liudmila S.

In: Frontiers in Genetics, Vol. 10, No. JUL, 736, 01.01.2019.

Research output: Contribution to journalArticle

Kendig, KI, Baheti, S, Bockol, MA, Drucker, TM, Hart, S, Heldenbrand, JR, Hernaez, M, Hudson, ME, Kalmbach, MT, Klee, EW, Mattson, NR, Ross, CA, Taschuk, M, Wieben, ED, Wiepert, M, Wildman, DE & Mainzer, LS 2019, 'SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy', Frontiers in Genetics, vol. 10, no. JUL, 736. https://doi.org/10.3389/fgene.2019.00736
Kendig, Katherine I. ; Baheti, Saurabh ; Bockol, Matthew A. ; Drucker, Travis M. ; Hart, Steven ; Heldenbrand, Jacob R. ; Hernaez, Mikel ; Hudson, Matthew E. ; Kalmbach, Michael T. ; Klee, Eric W ; Mattson, Nathan R. ; Ross, Christian A. ; Taschuk, Morgan ; Wieben, Eric D ; Wiepert, Mathieu ; Wildman, Derek E. ; Mainzer, Liudmila S. / SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy. In: Frontiers in Genetics. 2019 ; Vol. 10, No. JUL.
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