HLApers

HLApers performs allele-level HLA genotyping and expression quantification from RNA-seq data to enable analysis of HLA variation and its impact on phenotypes.

Key Features:

• Customized Reference Index: Uses the command hlapers prepare-ref to construct a reference index by replacing Gencode transcripts' HLA sequences with IMGT HLA allele sequences to reduce mapping bias.
• Adaptation of RNA-seq Tools: Adapts kallisto, Salmon, and STAR for HLA-specific analysis to infer genotypes and produce expression estimates.
• Allele-level Expression Quantification: Provides expression estimates for individual HLA alleles from RNA-seq data to support allele-specific analyses.

Scientific Applications:

• Genotype–phenotype association: Investigating correlations between HLA alleles and phenotypic traits using allele-level genotypes and expression.
• Disease research: Exploring the role of HLA variation in cancer and other diseases through allele-specific expression and genotyping.
• Personalized medicine: Linking HLA genotype and allele expression profiles to individual health outcomes.

Methodology:

Index preparation uses hlapers prepare-ref to build a reference by substituting IMGT HLA allele sequences into Gencode transcripts to improve mapping; data analysis employs adapted versions of kallisto, Salmon, and STAR for HLA genotyping and allele-level expression quantification from RNA-seq.