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 M. Chougule; Sharon Wei; Tingting Gao; Carl D. Green; Andrea Zuccolo; Doreen Ware; Jianwei Zhang; Kenneth L. McNally; Rod A. Wing

doi:10.1101/2023.06.25.546420

GenomicsbioRxivJun 25, 2023

Preprint

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

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

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.

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