Toil HLA

A toil wrapper that runs several HLA typing tools for Class I and Class II.

Tools

Tool Name	Repository
Lilac	https://github.com/hartwigmedical/hmftools/blob/master/lilac/README.md
HLAscan	https://github.com/SyntekabioTools/HLAscan
arcasHLA	https://github.com/RabadanLab/arcasHLA
seq2HLA	https://github.com/TRON-Bioinformatics/seq2HLA

Installing

After cloning the repo, create a virtual environment and run:

    # install package
    cd /path/to/repo && pip install .

Usage

The main command for this package is:

    toil_hla [TOIL-OPTIONS] [PIPELINE-OPTIONS]

This can be executed sequentially as follows:

1. Single machine mode

    toil_hla {OUTDIR}/jobstore \
        --stats \
        --disableCaching \
        --disableChaining \
        --rotatingLogging \
        --writeLogs {OUTDIR}/logs_toil \
        --logFile {OUTDIR}/head_job.toil \
        --statePollingWait 30 \
        --maxLocalJobs 500 \
        --outdir {OUTDIR} \
        --reference /path/to/reference/gr37.fasta \
        --normal-dna tests/data/test_DNA.bam \
        --normal-dna-id test_DNA \
        --tumor-rna /work/isabl/home/domenicd/tests/hla/test_files/test_RNA.bam \
        --tumor-rna-id test_RNA \
        --lilac-resource-dir /path/to/lilac/reference/immune \
        --lilac-img /path/to/lilac/run/script \
        --hlascan-tool /path/to/hlascan/hla_scan_r_v2.1.4 \
        --hlascan-resource-dir /path/to/hlascan/db/HLA-ALL.IMGT \
        --arcashla-img /path/to/arcasHLA/run/script \
        --seq2hla-img /path/to/seq2hla/run/script
   

2. To run in parallel on a high performance computing cluster add:

        --batchSystem custom_lsf
   

The Docker images used for testing can be pulled from here:

https://hub.docker.com/repository/docker/ddomenico/hmftools https://hub.docker.com/repository/docker/ddomenico/arcashla https://hub.docker.com/repository/docker/ddomenico/seq2hla

NOTE: Testing was done with singularity which can pull images from Dockerhub and build as *.sif or *.simg

The format of the /path/to/{TOOL}/run/script should look like one of these two implementations:

1. Singularity

    #!/bin/bash
    singularity exec --workdir {WORKDIR} --bind /local/system:/local/system hmftools.sif "$@"
   

2. Docker

    #!/bin/bash
    docker run -v /local/system:/local/system hmftools "$@"
   

The HLAscan tool and DB can be downloaded directly following the instructions here.

Testing

Test files have been provided in tests/data and corresponding tool outputs have been provided in tests/output. Test files were sources from GIAB for the test_DNA.bam and from arcasHLA for the test_RNA.bam. For the DNA, HG002 was downloaded and the BAM was then subset to the HLA A, B and C loci in order to generate a small file for test purposes. Here is the commands to generate:

    #!/bin/bash
    # Usage: ./subset_hla_regions.sh input_bam output_bam

    input_bam=$1
    output_bam=$2

    hla_regions="6:29910247-29944143 6:31321638-31349750 6:31236525-31283265"
    samtools view -b -o "${output_bam}" "${input_bam}" ${hla_regions}

Credits

This package was created using [Cookiecutter] and the [papaemmelab/cookiecutter-toil] project template.