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HLA

Summary Table

NAME CATEGORY CITATION
HLA-TAPAS HLA imputation pipeline Luo, Y., Kanai, M., Choi, W. et al. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 53, 1504–1516 (2021). https://doi.org/10.1038/s41588-021-00935-7
CookHLA HLA imputation tool Cook, S., Choi, W., Lim, H., Luo, Y., Kim, K., Jia, X., ... & Han, B. (2021). Accurate imputation of human leukocyte antigens with CookHLA. Nature Communications, 12(1), 1264.
DEEP*HLA HLA imputation tool Naito, T., Suzuki, K., Hirata, J., Kamatani, Y., Matsuda, K., Toda, T., & Okada, Y. (2021). A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes. Nature communications, 12(1), 1639.
HIBAG HLA imputation tool Zheng, X., Shen, J., Cox, C., Wakefield, J. C., Ehm, M. G., Nelson, M. R., & Weir, B. S. (2014). HIBAG—HLA genotype imputation with attribute bagging. The pharmacogenomics journal, 14(2), 192-200.
HLARIMNT HLA imputation tool Tanaka, K., Kato, K., Nonaka, N., & Seita, J. (2022). Efficient HLA imputation from sequential SNPs data by Transformer. arXiv preprint arXiv:2211.06430.
SNP2HLA HLA imputation tool Jia, X., Han, B., Onengut-Gumuscu, S., Chen, W. M., Concannon, P. J., Rich, S. S., ... & de Bakker, P. I. (2013). Imputing amino acid polymorphisms in human leukocyte antigens. PloS one, 8(6), e64683.

HLA imputation pipeline

HLA-TAPAS

  • NAME : HLA-TAPAS
  • CATEGORY : HLA imputation pipeline
  • SHORT NAME : HLA-TAPAS
  • FULL NAME : HLA-Typing At Protein for Association Studie
  • YEAR : 2021
  • DESCRIPTION : HLA-TAPAS (HLA-Typing At Protein for Association Studies) is an HLA-focused pipeline that can handle HLA reference panel construction (MakeReference), HLA imputation (SNP2HLA), and HLA association (HLAassoc).
  • URL : https://github.com/immunogenomics/HLA-TAPAS
  • CITATION : Luo, Y., Kanai, M., Choi, W. et al. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 53, 1504–1516 (2021). https://doi.org/10.1038/s41588-021-00935-7
  • KEYWORDS : HLA pipeline

HLA imputation tool

CookHLA

  • NAME : CookHLA
  • CATEGORY : HLA imputation tool
  • URL : https://github.com/WansonChoi/CookHLA
  • CITATION : Cook, S., Choi, W., Lim, H., Luo, Y., Kim, K., Jia, X., ... & Han, B. (2021). Accurate imputation of human leukocyte antigens with CookHLA. Nature Communications, 12(1), 1264.

DEEP*HLA

  • NAME : DEEP*HLA
  • CATEGORY : HLA imputation tool
  • URL : https://github.com/tatsuhikonaito/DEEP-HLA
  • CITATION : Naito, T., Suzuki, K., Hirata, J., Kamatani, Y., Matsuda, K., Toda, T., & Okada, Y. (2021). A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes. Nature communications, 12(1), 1639.

HIBAG

  • NAME : HIBAG
  • CATEGORY : HLA imputation tool
  • URL : https://github.com/zhengxwen/HIBAG
  • CITATION : Zheng, X., Shen, J., Cox, C., Wakefield, J. C., Ehm, M. G., Nelson, M. R., & Weir, B. S. (2014). HIBAG—HLA genotype imputation with attribute bagging. The pharmacogenomics journal, 14(2), 192-200.

HLARIMNT

  • NAME : HLARIMNT
  • CATEGORY : HLA imputation tool
  • SHORT NAME : HLARIMNT
  • FULL NAME : HLA Reliable IMputatioN by Transformer
  • YEAR : 2022
  • URL : https://github.com/seitalab/HLARIMNT
  • CITATION : Tanaka, K., Kato, K., Nonaka, N., & Seita, J. (2022). Efficient HLA imputation from sequential SNPs data by Transformer. arXiv preprint arXiv:2211.06430.
  • KEYWORDS : HLA, imputation

SNP2HLA

  • NAME : SNP2HLA
  • CATEGORY : HLA imputation tool
  • URL : http://software.broadinstitute.org/mpg/snp2hla/
  • CITATION : Jia, X., Han, B., Onengut-Gumuscu, S., Chen, W. M., Concannon, P. J., Rich, S. S., ... & de Bakker, P. I. (2013). Imputing amino acid polymorphisms in human leukocyte antigens. PloS one, 8(6), e64683.