Tutorial


※Imputation


MI-System accept the vcf.gz and plink format(.bed, .bim, .fam) files to upload, and allow users to upload through browser or url link(google drive)

※Notice that the files need to follow the rules:

  • Only contain single chromosome data
  • Coordinates version in hg19 (Except that using the hapmap3 as reference panels requires hg18)
  • Google drive url need to open the acesss right of the file

MI-System also provides two reference panels imputation:

  • Improved reference panels is the function that describes in IMPUTE2 ("Imputation with two phased reference panels") option
  • Merge reference panels is the function that describes in IMPUTE2 ("Imputation with two phased reference panels (merge reference panels)") option

Example file can download Chr22 example file

Tutorial document download: Tutorial document

※Tutorial video


1. login and functions:



2 Function Impute2:



3 Function impute5:



4 Function Beagle5:



5 Create Reference panel:



6 Split chromosome:



7 function liftover:



8 Download results:


※Citation


Please cite MI-System as follows:

Chattopadhyay, A., Lee, C. Y., Shen, Y. C., Lu, K. C., Hsiao, T. H., Lin, C. H., Lai, L. C., Tsai, M. H., Lu, T. P., & Chuang, E. Y. (2023). Multi-ethnic Imputation System (MI-System): a genotype imputation server for high-dimensional data. Journal of biomedical informatics, 104423. Advance online publication. https://doi.org/10.1016/j.jbi.2023.104423