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Thanks for your interest in the ricopili GWAS imputation and analysis pipeline. Installation instructions, documentation, and sample code can currently be found at:

https://sites.google.com/a/broadinstitute.org/ricopili/

Below are flowcharts detailing the implementation of the QC, PCA, and Imputation modules.

• QC (preimp_dir_[version]): workflow diagram
• PCA (pcaer_[version]): workflow diagram
• Imputation (impute_dirsub_[version]): workflow diagram

since fall 2018 a new installation process is in place that should in theory enable installation on many different computer environments without editing any souce code: please follow this: Ricopili Custom Installation