JAWAMix5 is an out-of-core open-source toolkit for association mapping using high-throughput sequence data. Taking advantage of its HDF5-based implementation, JAWAMix5 stores genotype data on disk and accesses them as though stored in main memory. Therefore, it offers a scalable and fast analysis without concerns about memory usage, whatever the size of the dataset. We have implemented eight functions for association studies, including standard methods (linear models, mixed linear models, rare variants test, nested association mapping (NAM), and local variance component analysis), as well as a novel Bayesian local variance component analysis. Application to real data reveals new biological insights and demonstrates that JAWAMix5 is reasonably fast compared to traditional solutions that load the complete dataset into memory, and that the memory usage is efficient regardless of the dataset size.
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Bioinformatics. 2013 May 1;29(9):1220-2. doi: 10.1093/bioinformatics/btt122. Epub 2013 Mar 11.
JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models.
Long Q, Zhang Q, Vilhjalmsson BJ, Forai P, Seren ü, Nordborg M.