This repository is no longer actively maintained, as we have introduced Imputation Server 2.
Please visit our new repository: genepi/imputationserver2.
Thank you for your continued support and contributions!
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 http://imputationserver.readthedocs.io.
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.
- Lukas Forer
- Sebastian Schönherr
- Sayantan Das
- Christian Fuchsberger
Project contributions are more than welcome! See our CONTRIBUTING.md file for details.