FAQ

Q. What's the difference between HLA-TAPAS and SNP2HLA?

A. HLA-TAPAS is an updated version of the SNP2HLA (also developed by our group) to build an imputation reference panel, perform HLA classical allele, amino acid and SNP imputation within the extended MHC region. Briefly, major updates include (1) using PLINK1.9 instead of v1.07; (2) using BEAGLE v4.1 instead of v3 for phasing and imputation; and (3) including custom R scripts for performing association and fine-mapping analysis at amino acid level in multiple ancestries.

Q. What is the genomic build of the released reference panel?

A. The current HLA imputation panel described in our work is build on GRCh37/hg19. We are working on have a GRCh38 release soon. But the current MakeReference pipeline can handle GRCh38 coding, so please feel free to build your own GRCh38 HLA reference panel!