Speeding up eQTL scans in the BXD population using GPUs.

ABSTRACT: The BXD family of mouse strains are an important reference population for systems biology and genetics that have been fully sequenced and deeply phenotyped. To facilitate interactive use of genotype-phenotype relations using many massive omics data sets for this and other segregating populations, we have developed new algorithms and code that enable near-real-time whole-genome quantitative trait locus (QTL) scans for up to one million traits. By using easily parallelizable operations including matrix multiplication, vectorized operations, and element-wise operations, our method is more than 700 times faster than a R/qtl linear model genome scan using 16 threads. We used parallelization of different CPU threads as well as GPUs. We found that the speed advantage of GPUs is dependent on probl

SUBMITTER: Trotter C 

PROVIDER: S-EPMC8664437 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature