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 (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

Please contact the HPC staff (staff@hpc.nih.gov) if you want additional reference files installed for HLA-LA. Note that HLA-LA will break for all users if your reference file is incorrectly formatted. See this documentation for the format. We highly recommend using an already installed reference as a template. For example:

[user@cn3144 ~] module load HLA-LA
[user@cn3144 ~] cd $HLA_LA_GRAPHS/PRG_MHC_GRCh38_withIMGT/knownReferences
[user@cn3144 knownReferences] head PRG_MHC_GRCh38_withIMGT.txt > ~/testgraph.txt
[user@cn3144 knownReferences] tail PRG_MHC_GRCh38_withIMGT.txt >> ~/testgraph.txt

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
[+] Loading singularity  3.10.5  
[+] Loading HLA-LA  1.0.3 

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

[user@cn3144 46116226]$ cp $HLA_LA_TESTDATA/NA12878.mini.cram  .

[user@cn3144 46116226]$ samtools index NA12878.mini.cram

[user@cn3144 46116226]$ HLA-LA.pl --BAM NA12878.mini.cram \
      --graph PRG_MHC_GRCh38_withIMGT --sampleID NA12878 \
	    --maxThreads 7 --workingDir .
HLA-LA.pl

Identified paths:
        samtools_bin: /opt/conda/envs/hla-la/bin/samtools
        bwa_bin: /opt/conda/envs/hla-la/bin/bwa
        java_bin: /opt/conda/envs/hla-la/bin/java
        picard_sam2fastq_bin: /opt/conda/envs/hla-la/bin/picard
        General working directory: /lscratch/4506949
        Sample-specific working directory: /lscratch/4506949/NA12878

Using /opt/conda/envs/hla-la/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences/1000G_B38.txt as reference file.
Extract reads from 534 regions...
Extract unmapped reads...
Merging...
Indexing...
Extract FASTQ...
        /opt/conda/envs/hla-la/bin/picard SamToFastq VALIDATION_STRINGENCY=LENIENT I=/lscratch/4506949/NA12878/extraction.bam F=/lscratch/4506949/NA12878/R_1.fastq F2=/lscratch/4506949/NA12878/R_2.fastq FU=/lscratch/4506949/NA12878/R_U.fastq 2>&1

Now executing:
../bin/HLA-LA --action HLA --maxThreads 7 --sampleID NA12878 --outputDirectory /lscratch/4506949/NA12878 --PRG_graph_dir /opt/conda/envs/hla-la/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT --FASTQU /lscratch/4506949/NA12878/R_U.fastq.splitLongReads --FASTQ1 /lscratch/4506949/NA12878/R_1.fastq --FASTQ2 /lscratch/4506949/NA12878/R_2.fastq --bwa_bin /opt/conda/envs/hla-la/bin/bwa --samtools_bin /opt/conda/envs/hla-la/bin/samtools --mapAgainstCompleteGenome 1 --longReads 0
Set maxThreads to 7

[...]

[user@cn3144 46116226]$ 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