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

Documentation

The documentation is available at http://imputationserver.readthedocs.io.

Citation

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).

Contact

Feel free to contact us in case of any problems.

Contributors

• Lukas Forer
• Sebastian Schönherr
• Sayantan Das
• Christian Fuchsberger

Contributing

Project contributions are more than welcome! See our CONTRIBUTING.md file for details.