A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"
The tutorial consists of two parts:
- #1. HLA imputation : We introduce protocols to QC genotype, perform haplotype phasing and HLA imputation. We provide useful scripts and example usage, with example genotype and reference datasets.
- #2. HLA association and fine-mapping: We introduce various statistical methods to identify and fine-map disease-associated HLA variations. The HLA imputation results from section #1 will be used. We provide useful scripts with some example phenotype data.