software pipeline for performing genome wide association studies


PIQUE is a software pipeline for performing genome wide association studies (GWAS). The main function of PIQUE is to provide ‘convenience’ wrappers that allow users to perform GWAS using the popular program EMMAX (Kang et al., 2010) without the need to be familiar with all of the software tools used to generate the required EMMAX input files. PIQUE will also perform a number of quality control steps prior to running EMMAX, ensuring that the various input data files are in the correct format. PIQUE proceeds in two main stages although there are multiple entry and exit points from which the pipeline can be run. The first stage consists of running the “pique-input” program, which can read genotype and phenotype information in several different formats and generates all the necessary input files required to run EMMAX. The second step in the pipeline uses the “pique-run” program to actually run EMMAX using the files generated by “pique-input” (or pre-existing user-supplied input files) to perform the GWAS and output the analysis summary files.

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