We have developed the following tools for setting up and conducting a federated meta-analysis:

• A Standard Operating Procedure for setting up the server and preparing data for federated meta-analysis
• Example code from the exemplar projects for running a federated meta-analysis

The exemplar projects required extensive work to harmonise exposures and outcomes across a wide range of studies and coding of algorithms to convert the data to common standard. These harmonisation algorithms and the associated meta-data are made available for re-use via the InterConnect registry harmonisation catalogue.

The project has also investigated methods for studying populations that are genetically diverse. Methods that leverage genetic heterogeneity, rather than suppressing or simply accounting for it, have been identified. Software for admixture and identity-by-descent (IBD) mapping are available and continue to be developed.

Links to some of the currently used admixture mapping software

• HAPMIX: http://www.stats.ox.ac.uk/~myers/software.html
• LAMP: Local Ancestry in adMixed Populations, http://lamp.icsi.berkeley.edu/lamp/
• MULTIMIX: https://jmarchini.org/multimix/
• PCADMIX: https://sites.google.com/site/pcadmix/home
• RFMix: https://sites.google.com/site/rfmixlocalancestryinference/
• SupportMix: http://mezeylab.cb.bscb.cornell.edu/Software.aspx

Current software that can be used for IBD mapping

• BEAGLE: http://faculty.washington.edu/browning/beagle/beagle.html
• DASH: http://www1.cs.columbia.edu/~gusev/dash/
• GERMLINE: http://www.cs.columbia.edu/~gusev/germline/
• PLINK: http://zzz.bwh.harvard.edu/plink/ibdibs.shtml