CloudAssoc: A Pipeline for Imputation Based Genome Wide Association Study on Cloud

Genome wide association study (GWAS) has been proved to be an efficient approach to identify susceptibility genes for complex diseases. In order to increase the power for detecting the disease causal variants, imputation has been used to predict genotype dosages of untyped variants on the basis of linkage disequilibrium evaluated by public data. However, as the volume of data grows, time-consuming of imputation based association study becomes extremely large. We developed a cloud based pipeline to implement data format conversion, imputation, quality control and association study based on Map/Reduce framework which can aid biologists to accelerate the identification and evaluation of susceptibility genes for complex diseases and make it easier to combine GWAS data from worldwide for meta analysis.