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xHLA: Fast and accurate HLA typing from short read sequence data

The Human Leukocyte Antigen (HLA) gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome, and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. xHLA iteratively refines the mapping results at the amino acid level to achieve 99 to 100% 4-digit typing accuracy for both class I and II HLA genes, taking only about 3 minutes to process a 30X whole genome BAM file on a desktop computer.

Installation

Compile docker image:

cd docker
make build
make deploy

Usage

Run xHLA caller directly on an indexed BAM file generated using BWA-mem against hg38 reference without alt contigs:

docker run -v `pwd`:`pwd` -w `pwd` docker-dev.hli.io/xchao/hla \
    --sample_id test --input_bam_path test.bam \
    --output_path test

For other types of BAMs, pre-processing is required. Please check details here.

Output is a JSON file that lists 12 HLA alleles, 2 for each of the HLA genes:

{
 "subject_id": "176444255",
 "creation_time": "2016-05-04T08:25:04Z",
 "report_version": "1.1",
 "report_type": "hla_typing",
 "sample_id": "176444255",
 "hla": {
  "alleles": [
   "A*01:01",
   "A*02:01",
   "B*13:02",
   "B*37:01",
   "C*06:02",
   "C*06:02",
   "DPB1*04:01",
   "DPB1*04:01",
   "DQB1*02:02",
   "DQB1*05:01",
   "DRB1*07:01",
   "DRB1*10:01"
  ]
 }
}

Citation

Xie et al. (2017) Fast and accurate HLA typing from short-read next-generation sequence data with xHLA. PNAS doi:10.1073/pnas.1707945114