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Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
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This repository includes the complete source code for the Michigan Imputation Server workflow based on Minimac4. The workflow itself is executed with the Cloudgene workflow system for Hadoop MapReduce.

Michigan Imputation Server consists of several parallelized pipeline steps:

  • Quality Control
  • QC Report
  • Phasing and Imputation
  • Compression and Encryption


The documentation is available at


The release cycle is described here.


Please cite this paper if you use Michigan Imputation Server:

Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze S, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C. Next-generation genotype imputation service and methods. Nature Genetics 48, 1284–1287 (2016).


Feel free to contact us in case of any problems.

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