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Sanger Imputation Service

Sanger Imputation Service

Sanger genotype imputation and phasing service is a web-based tool at Wellcome Sanger Institute. The service pipeline uses EAGLE2 or SHAPEIT2 for pre-phasing, EAGLE2 for phasing, and PBWT (Positional Burrows-Wheeler Transform) for genotype imputation. The service currently offers the following reference panels: 1. Haplotype Reference Consortium, 2. African Genome Resources, 3. 1000 Genomes Phase 3, 4. UK10K, 5. UK10K + 1000 Genomes Phase 3.

Topic

Population genomics

Details

  • Operation: Phasing; Imputation
  • Input: VCF or 23andMe format
  • Output: VCF, tarball of logs
  • Software interface: Web user interface
  • Language: -
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Other
  • Cost: Free
  • Version name: -
  • Maturity: beta
  • Credit: ERC, Wellcome Trust
  • Contact: vr-impute _at_ sanger.ac.uk
  • Collection: -

Publications

McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R "A reference panel of 64,976 haplotypes for genotype imputation." Nat Genet. 2016 Oct;48(10):1279-83. https://doi.org/10.1038/ng.3643
PMID: 27548312
PMCID: PMC5388176

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