HLA-HAT: HLA Haplotype Analysis Toolkit

The HLA Haplotype Analysis Toolkit (HLA-HAT) was designed to support analysis of the human leukocyte antigen (HLA) genes in the allele-specific context. The polymorphic nature of these genes makes it especially difficult to analyze and visualize allele-specific information in the context of the linear, haploid reference genome. Thus, HLA-HAT implements HISAT2 and HISAT-genotype for the extraction and typing from HLA reads and constructs a custom reference HLA genome for downstream variant calling, allelic imbalance quantitation, and additional analysis.

The User Guide

This documentation describes how to get started with HLA-HAT, including the extraction, assignment, and downstream analysis of HLA allele-specific sequencing reads.

• Introduction
  • HLA Annotation and Nomenclature
  • Bioinformatics Tools
• Usage
  • Docker
  • R
  • WDL
  • Terra
• Analysis
  • Module 1. Preparation and assignment
    • HLA read extraction
    • HLA typing
  • Module 2. Reference Generation
    • HLA haplotype reporting
    • Create HLA reference FASTA
    • Align HLA reads
  • Module 3. Downstream Analysis
    • Generate HLA-associated alignment metrics
    • Quantifying allelic imbalance
    • Paired tumor-normal data
    • Tumor-only datasets
    • Variant detection
• Resources
• References