HLA*LA carries out HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph. Previously called HLA*PRG:LA, the application was developed by Alexander Dilthey at NHGRI.

Reference:

• Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb, Shabir A Madhi, Arang Rhie, Sergey Koren, Seiamak Bahram, Gil McVean, Adam M Phillippy HLA*LA—HLA typing from linearly projected graph alignments.Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4394–4396

• Github Site
• Description of the algorithm

• Module Name: HLA-LA or HLA-PRG-LA (see the modules page for more information)
• Multithreaded.
• Environment variables set
  • HLA_LA_GRAPHS HLA*LA Graph References
  • HLA_LA_TESTDATA HLA*LA Test Data
• Additional References are linked under $HLA_LA_GRAPHS/additionalReferences/

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres=lscratch:50 --cpus-per-task=8 --mem=60g 
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load HLA-LA
[+] HLA-PRG-LA is called HLA-LA as of Jan 2019. Either name can be used when loading the module
[+] Loading HLA-LA  1.0.1 on cn3144
[..]

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOBID

[user@cn3144 ~]$ cp $HLA_LA_TESTDATA/NA12878.mini.cram  .

[user@cn3144 ~]$ samtools index NA12878.mini.cram

[user@cn3144 ~]$ HLA-LA.pl --BAM NA12878.mini.cram \
      --graph PRG_MHC_GRCh38_withIMGT --sampleID NA12878 \
	    --maxThreads 7 --workingDir .
Identified paths:
    samtools_bin: /usr/local/apps/samtools/1.9/bin/samtools
    bwa_bin: /usr/local/apps/bwa/0.7.17/bwa
    java_bin: /usr/bin/java
    picard_sam2fastq_bin: /usr/local/apps/picard/2.9.2/build/libs/picard.jar
    General working directory: /lscratch/43090316
    Sample-specific working directory: /lscratch/43090316/NA12878

Extract reads from 534 regions...
Extract unmapped reads...
Merging...
Indexing...
Extract FASTQ...
        /usr/bin/java -Xmx10g -XX:-UseGCOverheadLimit -jar ...
Now executing:
../bin/HLA-LA --action HLA --maxThreads 4 --sampleID NA12878 ...
Set maxThreads to 4

[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. HLA.sh). For example:

#!/bin/bash
set -e
cd /lscratch/$SLURM_JOBID
module load HLA-LA

cp /data/$USER/myfile.cram .
samtools index myfile.cram

cpus=$(( SLURM_CPUS_PER_TASK - 1 ))
echo "Running on $cpus CPUs"
HLA-LA.pl --BAM myfile.cram --graph PRG_MHC_GRCh38_withIMGT --sampleID myfile --maxThreads $cpus --workingDir .

# copy output from /lscratch back to /data area
cp -r myfile/hla  /data/$USER/

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=32 --mem=100g --gres=lscratch:100 --time=1-00:00:00 HLA.sh