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

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

bioRxiv (Cold Spring Harbor Laboratory)（2023）

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摘要

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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关键词

genome variant,hpc-based,hpc-gvcw

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