Due to TCGA privacy concerns, the password for HLA allele data is provided only to researchers who have access to the primary sequence data from the TCGA. Please contact us at haoye.ecust@gmail.com or qiliu@tongji.edu.cn
Eight hla genotyping tools with default parameter were used to process the TCGA WES datasets.
| Tools | URL | version |
|---|---|---|
| POLYSOLVER | https://hub.docker.com/r/sachet/polysolver/tags | v4 |
| OptiType | https://hub.docker.com/r/fred2/optitype/tags | v1.3.1 |
| xHLA | https://hub.docker.com/r/humanlongevity/hla/tags | DIGEST:425487b52034 |
| HLA-HD | https://www.genome.med.kyoto-u.ac.jp/HLA-HD/ | v1.2.0.1 |
| hla-genotyper | https://pypi.org/project/hla-genotyper/ | v0.4.2b1 |
| SOAP-HLA | http://soap.genomics.org.cn/SOAP-HLA.html | v2.2 |
| HLA-VBSeq | http://nagasakilab.csml.org/hla/ | v2 |
| Kourami | https://github.com/Kingsford-Group/kourami | v0.9.6 |
| LOHHLA | https://hub.docker.com/r/mleventhal/lohhla/tags | DIGEST:60253161bf8e |
Li, X., Zhou, C., Chen, K., Huang, B., Liu, Q. and Ye, H. (2021), Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy. Mol Oncol. https://doi.org/10.1002/1878-0261.12895 PMID:33411982