Sanger Imputation Service

Sanger Imputation Service

Sanger Imputation Service


This is a free genotype imputation and phasing service provided by the Wellcome Trust Sanger Institute. You can upload GWAS data in VCF or 23andMe format and receive imputed and phased genomes back. Optional pre-phasing is with EAGLE2 or SHAPEIT2 and imputation is with PBWT into a choice of reference panels including 1000 Genomes Phase 3, UK10K, and the Haplotype Reference Consortium.

Who is this for? This service is aimed at researchers wanting to impute many thousands of GWAS samples against a consistent reference in a consistent manner. The PBWT algorithm is extremely fast and efficient for this purpose. We do support genotype data from few samples, such as 23andMe data from individuals, however the overhead of data transfer via Globus is aimed at the larger files produced by imputing into large GWAS datasets from large reference panels.

Download and Installation

The service and instructions on how to use it are available at


Sanger Contributors


  • A reference panel of 64,976 haplotypes for genotype imputation.

    McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR et al.

    Nature genetics 2016;48;10;1279-83

  • Reference-based phasing using the Haplotype Reference Consortium panel.

    Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y et al.

    Nature genetics 2016;48;11;1443-1448

  • Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).

    Durbin R

    Bioinformatics (Oxford, England) 2014;30;9;1266-72