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bioRxiv · 10.1101/2021.11.16.468610

FastQTLmapping: an ultra-fast package for mQTL-like analysis

Gao, X.·Li, J.·Liu, X.·Peng, Q.·Jing, H.·Wang, S.·Liu, F.
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Abstract

SummaryHere we describe fastQTLmapping, a C++ package that is computationally efficient not only for mQTL-like analysis but as a generic solver also for conducting exhaustive linear regressions involving extraordinarily large numbers of dependent and explanatory variables allowing for covariates. Compared to the state-of-the-art MatrixEQTL, fastQTLmapping was an order of magnitude faster with much lower peak memory usage. In a large dataset consisting of 3,500 individuals, 8 million SNPs, 0.8 million CpGs and 20 covariates, fastQTLmapping completed the mQTL analysis in 7 hours with 230GB peak memory usage. Availability and ImplementationFastQTLmapping is implemented in C++ and released under a GPL license. FastQTLmapping can be downloaded from https://github.com/TianTTL/xQTLmapping. Contactliufan@big.ac.cn

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Gao, X., Li, J., Liu, X., Peng, Q., Jing, H., Wang, S., Liu, F.. 2021-11-19. FastQTLmapping: an ultra-fast package for mQTL-like analysis. https://doi.org/10.1101/2021.11.16.468610

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