(preprint) HPC-based genome variant calling workflow (HPC-GVCW)


Yong Zhou, Nagarajan Kathiresan, Zhichao Yu, Luis F. Rivera, Manjula Thimma, Keerthana Manickam, Dmytro Chebotarov, Ramil Mauleon, Kapeel Chougule, Sharon Wei, Tingting Gao, Carl D. Green, Andrea Zuccolo, Jianwei Zhang, Doreen Ware, Kenneth L. McNally,
Rod A Wing

bioRxiv 2023.06.25.546420

This article is a preprint and has not been certified by peer review [what does this mean?].

Preprinted:  June 26, 2023


A high-performance computing genome variant calling workflow was designed to run GATK on HPC platforms.  This workflow efficiently called an average of 27.3 M, 32.6 M, 168.9 M, and 16.2 M SNPs for rice, sorghum, maize, and soybean, respectively, on the most recently released high-quality reference sequences.  Analysis of a rice pan-genome reference panel revealed 2.1 M novel SNPs that have yet to be publicly released.

Competing Interest Statement

The authors have declared no competing interest.




HPC-based genome variant calling workflow (HPC-GVCW)

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