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.