arcasHLA: high resolution HLA typing from RNA seq. arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.

• https://github.com/RabadanLab/arcasHLA

• Module Name: arcashla (see the modules page for more information)
• example : /usr/local/apps/arcashla/0.5.0/test

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

[user@biowulf]$ sinteractive --mem=5g --cpus-per-task=4
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 arcashla
[user@cn3144 ~]$ cd /data/$USER/
[user@cn3144 ~]$ cp -r /usr/local/apps/arcashla/0.5.0/test .
[user@cn3144 ~]$ arcasHLA extract test/test.bam -o test/output -t $SLURM_CPUS_PER_TASK
[user@cn3144 ~]$ arcasHLA genotype test/output/test.extracted.1.fq.gz test/output/test.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o test/output -t $SLURM_CPUS_PER_TASK
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load arcashla
cd /data/$USER/test
arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK
arcasHLA genotype output/test.extracted.1.fq.gz output/test.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o output -t $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] [--cpus-per-task=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK
cd dir2; arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK
cd dir3; arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f job.swarm [-g #] [-t #] --module arcashla