Michigan Imputation Server 2
Free Next-Generation Genotype Imputation Platform

Michigan Imputation Server 2 provides a free genotype imputation service (chromosomes 1-22, chromosome X and HLA region) using Minimac4. You can upload phased or unphased GWAS genotypes and receive phased and imputed genomes in return. Our server supports imputation from numerous reference panels. For all uploaded datasets a comprehensive QC is performed. The complete source code is hosted on GitHub.

Please cite this paper if you use Michigan Imputation Server 2:

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).

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Latest News

19 September 2024
We have successfully migrated to a new architecture and released Michigan Imputation Server 2. Please note the major change regarding allele swaps!
Learn more.

21 May 2021
We have increased the max sample size to 110k.

15 April 2021
Update to new framework completed! Currently, max sample size will be limited to 25k, but we expect to lift this limitation in the next few weeks.

18 March 2020
Due to coronavirus-related impacts support may be slower than usual. If you haven't heard back from us after a week or so, feel free to e-mail again to check on the status of things. Take care!

07 November 2019
Updated MIS to v1.2.4! Major improvements: Minimac4 for imputation, improved chrX support, QC check right after upload, better documentation. Checkout out our GitHub repository for further information.

17 October 2019
Michigan Imputation Server at ASHG19. All information is available here.

27 November 2018
Redesigned user interface to improve user experience.

27 June 2017
Updated pipeline to v1.0.2. Release notes can be found here.

29 Aug 2016
Imputation server paper is out now: Das et al., Nature Genetics 2016

19 April 2016
Updated HRC Panel (r1.1) available.

12 January 2016
New Reference Panel (CAAPA) available.

24 April 2015
HRC release 1 (64,976 haplotypes at 39,235,157 SNPs) is now ready for use for HRC consortium members.