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Workflow for quantification of HLA-I allele-specific expression loss using arcasHLA-quant. The pipeline takes RNA-seq data from tumor, and WES data from tumor and normal samples. The major steps include (1) HLA-I genotyping; (2) HLA-I gene expression quantification using arcasHLA-quant and allele frequency calculation; (3) tumor purity and ploidy estimation; and (4) adjustment of allele frequencies for HLA-I ASE inference
