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The 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 high typing accuracy for both class I and II HLA genes.

References:

• Chao Xiea, Zhen Xuan Yeo, Marie Wong, Jason Piper, Tao Long, Ewen F. Kirkness, William H. Biggs, Ken Bloom, Stephen Spellman, Cynthia Vierra-Green, Colleen Brady, Richard H. Scheuermann, Amalio Telenti, Sally Howard, Suzanne Brewerton, Yaron Turpaz, and J. Craig Venter, Fast and accurate HLA typing from short-read next-generation sequence data with xHLA, Proc. Natl. Acad. Sci. USA, 2017, vol. 114, N30, p. 8059–8064

• xHLA Github page

• Module Name: xHLA (see the modules page for more information)
• Multithreaded
• Unusual environment variables set
  • XHLA_HOME  xHLA installation directory
  • XHLA_BIN       xHLA executable directory
  • XHLA_TEST    xHLA example directory
  • XHLA_DATA    xHLA data directory
• Example file in $XHLA_TEST

IMPORTANT NOTE: Before submitting a job running xHLA software to cluster, user(s) should estimate the amount of memory required for running the job by benchmarking their data.

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

[user@biowulf]$ sinteractive --mem=16g --cpus-per-task=14 --gres=lscratch:40
[user@cn3316 ~]$ module load xHLA
[user@cn3316 ~]$ git clone https://github.com/humanlongevity/HLA.git
[user@cn3316 ~]$ mkdir test_run
[user@cn3316 ~]$ xhla --sample_id test --input_bam_path HLA/tests/test.bam --output_path test_run
[07/Feb/2018 15:09:25] INFO - Xie Chao's HLA typing algorithm
[07/Feb/2018 15:09:25] INFO - Sample_id: test Input file: HLA/tests/test.bam
typer.sh parameters: DELETE=false FULL=false
Extracting reads from S3
...
done lpsolve
 [1] "A*01:01"    "A*02:01"    "B*13:02"    "B*37:01"    "C*06:02"   
 [6] "DPB1*04:01" "DQB1*02:01" "DQB1*05:01" "DRB1*07:01" "DRB1*10:01"
pulling non-core exons in
  DQB1*02:01   DQB1*02:01 
"DQB1*02:02" "DQB1*02:12" 
named character(0)
refining solution
        allele rank
 1:    A*01:01  6.0
 2:    A*02:01  3.0
 3:    B*13:02 48.5
 4:    B*37:01 96.0
 5:    C*06:02 10.0
 6: DPB1*04:01   NA
 7: DQB1*02:02   NA
 8: DQB1*05:01 12.0
 9: DRB1*07:01  9.0
10: DRB1*10:01 72.5
     allele rank field1 field2
1:  A*01:01    6      1      1
2: A*01:01L   NA      1      1
3: A*01:01N   NA      1      1
4:  A*01:32   NA      1     32
5:  A*01:45   NA      1     45
6: A*01:56N   NA      1     56
7: A*01:103   NA      1    103
8: A*01:177   NA      1    177
...
Reporting
[07/Feb/2018 15:18:50] INFO - Successfully wrote output file
[07/Feb/2018 15:18:50] INFO - HLA typing: shutting down.
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Note that the command xhla will accept both the relative and absolute paths to the input data.

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

#!/bin/bash
module load xHLA
mkdir HLA/test
xhla --sample_id test --input_bam_path HLA/tests/test.bam --output_path HLA/test

Submit this job using the Slurm sbatch command.

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