JAWAMix5 stands for HDF5-based JAva implementation of Whole genome Association studies using Mixed model. The motivation of developing JAWAMix5 is to provide a platform-independent toolkit for mixed model-based association mapping that is scalable for very large dataset. It also supports simulation-based power estimations We intend to offer long-term maintenance for JAWAMix5 and continue adding our new developments into it.
In its current release, we provide 9 functions.
The toolkit is a batteries-included executable, therefore no installation is needed. Just copy the executable, jawamix5.jar, and run it using the standard command for java packages:
java –Xmx2g –jar /path/to/jawamix5.jar
This will prompt a help message. If that does not happen, please be so kind as to send us an email.
We provide ten analytical functions in version r1.1.0, the first release of JAWAMix5:
(1) An approximation of the original mixed model (Kang, Zaitlen et al. 2008), i.e., EMMAX (Kang, Sul et al. 2010)); (2) Local variance component analysis by traditional point estimations (Yang, Benyamin et al. 2010), however jointly accounting for population structure; (3) Local variance component analysis by Bayesian estimations; (4) Rare variants analysis using collapsing test (Li and Leal 2008) with or without population structure controlled; (5) Standard linear regression without mixed model; (6) Standard stepwise regression without mixed model; (7) Stepwise regression based on mixed model; (8) Nested Association Mapping (NAM). (McMullen, Kresovich et al. 2009). (9) Simulation-based Power Estimation for the design of Rare Disease sequencing studies
In addition to main analysis, we also provide assistant functions: (1) Calculate kinship for the whole genome or particular regions; (2) Import the input genome files (in CSV format) to HDF5 format; (3) Change the ACGT coded genotypes into number-coded genotypes and, by the way, filter out some non-qualified variants.
All the functions are used as:
java –Xmx2g –jar /path/to/jawamix5.jar function <options>
The details of the options of each function can be found in the detailed users manual.