Sanger Imputation Service

A free genotype imputation and phasing service provided by the Wellcome Sanger Institute.

This is a free genotype imputation and phasing service provided by the Wellcome 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.

Contact

If you need help or have any queries, please contact us using the details below.


Sanger Institute Contributors

Photo of Dr Shane A. McCarthy

Dr Shane A. McCarthy

Senior Scientific Manager