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HLA Typing Pipeline Specification

Pipeline Details

  • Name: HLA_typing
  • Pipeline UUID: s0ki8cd82jwjlhegscpueyxhi3wwyi
  • Version: 1.0.1
  • View Pipeline:

Overview

HLA Typing pipeline is designed for predicting neoantigens from tumor and normal samples (WES or WGS) and RNA-seq data (optional) from tumor. It performs HLA class I genotyping from high-throughput sequencing data using OptiType, a state-of-the-art algorithm for precise HLA typing from DNA or RNA sequencing reads.

Key Use cases:

  • HLA Class I Genotyping: Accurate 4-digit HLA genotyping predictions for HLA-A, HLA-B, and HLA-C loci from NGS data.
  • Neoantigen Prediction: Supporting workflow for identifying potential neoantigens in cancer immunotherapy research.
  • Immunogenomics Research: HLA typing for population genetics studies and personalized medicine applications.

Features

  • Support for Multiple Input Types: Accepts both DNA and RNA sequencing data with configurable data type parameter.
  • Flexible Input Format Support: Handles both single-end and paired-end FASTQ files seamlessly.
  • High Precision Algorithm: Uses OptiType's integer linear programming approach for accurate 4-digit HLA genotyping.
  • Comprehensive Output: Generates detailed results including allele predictions, confidence scores, and coverage visualizations.
  • Containerized Execution: Utilizes Docker container (quay.io/mustafapir/optitype:1.3.0) for reproducible results across different environments.
  • IMGT/HLA Database Integration: Leverages the latest IMGT/HLA reference database for allele matching.

Input/Output Specification

Inputs

Required

reads

  • Description: Primary sequencing reads file containing raw sequencing data for HLA typing analysis.
  • Format: FASTQ (.fastq or .fastq.gz)
  • Example File Path: /path/to/input/sample_R1.fastq.gz

mate

  • Description: Mate pair sequencing reads file for paired-end sequencing data.
  • Format: FASTQ (.fastq or .fastq.gz)
  • Example File Path: /path/to/input/sample_R2.fastq.gz

Optional Inputs

Data Type Parameter

  • Description: Specifies whether the input sequencing data is from DNA or RNA sources.
  • Options: "dna" or "rna"
  • Default: "rna"
  • Format: String parameter

Outputs

Reported Outputs

  • csvFile:
  • Description: Table of predicted HLA alleles with confidence scores and detailed typing results
  • Format: .csv/.tsv
  • Example File Path: /output/directory/sample_result.tsv

  • Location: Main output folder

  • outputFilePdf:

  • Description: Coverage visualization plots showing alignment coverage for each predicted HLA allele
  • Format: .pdf
  • Example File Path: /output/directory/sample_coverage_plot.pdf
  • Location: Main output folder

Supporting Outputs

  • bamFile:
  • Description: Aligned BAM file containing HLA-specific read alignments used for genotyping
  • Format: .bam
  • Example File Path: /output/directory/sample_aligned.bam

Associated Processes

References & Additional Documentation