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

Detail

  • Operation: Phasing;Imputation

  • Software interface: Web user interface

  • Language: -

  • License: Other

  • Cost: Free

  • Version name: -

  • Credit: ERC, Wellcome Trust

  • Input: VCF or 23andMe format

  • Output: VCF, tarball of logs

  • Contact: vr-impute@sanger.ac.uk

  • Collection: -

  • Maturity: beta

Publications

  • A reference panel of 64,976 haplotypes for genotype imputation.
  • McCarthy S, et al. A reference panel of 64,976 haplotypes for genotype imputation. A reference panel of 64,976 haplotypes for genotype imputation. 2016; 48:1279-83. doi: 10.1038/ng.3643
  • https://doi.org/10.1038/ng.3643
  • PMID: 27548312
  • PMC: PMC5388176

Download and documentation

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