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,
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This article is a preprint and has not been certified by peer review [what does this mean?].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 |
Abstract
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.
2023.06.25.546420v1.full_.pdf
HPC-based genome variant calling workflow (HPC-GVCW)
