UPDG: Utilities package for data analysis of Pooled DNA GWAS

UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background.UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.Over the years, many methods and algorithms have been developed for genetic association studies. With the availability of DNA microarrays and their common use in genomewide association study (GWAS), the dramatic increase in the number of markers to be handled poses a great challenge to the data analysis. Owing to the inability to analyze GWAS data manually, useful computer programs have been developed, but are mainly focused on the application for GWAS based on analysis of individual DNA samples (hereafter called individual DNA GWAS). Despite being a well-established strategy for c