Goals and use of h3agwas

#Goals of the h3agwas pipeline

The goals of this pipeline is to have a portable and robust pipeline for performing a genome-wide association study

There are three separate workflows that make up h3agwas

• Conversion of raw Affymetrix CEL files to PLINK calls. In the next version, we'll also support Illumina idat files.

• Quality control of the data. This is the focus of the pipeline. It takes as input either PLINK files or Illumina

• Association study. A simple analysis association study is done. The purpose of this is to give users an introduction to their data. Real studies, particularly those of the H3A consortium will have to handle compex co-variates and particular population study. We encourage users of our pipeline to submit thieir analysis for the use of other scientists.