HLA genotyping

This page describes genotype HLA alleles using graphtyper. The data required is downloaded from the latest release which describes the variation in the HLA alleles. Only GRCh38 is supported.

## Get the HLA data directory
wget https://github.com/DecodeGenetics/graphtyper/releases/download/v2.7.4/HLA_data.tar.gz

## Extract the HLA data into a directory called "data"
mkdir -p data
tar -xzf HLA_data.tar.gz -C data 

## Set paths
GRAPHTYPER=/path/to/graphtyper
GENOME=/path/to/genome.fa
BAMLIST=/path/to/list/of/bams.txt
THREADS=<number of threads>

## Run HLA typing
while read chr begin end gene; do
  echo "${GRAPHTYPER} genotype_hla ${GENOME} data/${gene}.vcf.gz --region=${chr}:${begin}-${end} --sams=${BAMLIST} --verbose --threads=${THREADS}"
done < data/regions.tsv | bash

Instead of piping into bash, which will genotype serially, you can run the commands in parallel, ie. in GNU parallel or slurm.