HLA-typing using HLA-LA tool (Nextflow pipeline)

Introduction

The pipeline does Human Leukocyte Antigen (HLA) typing using HLA-LA. See the Paper and the GitHub repo.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker and singularity containers making installation trivial and results highly reproducible.

The pipeline takes in bam files as input. As a prerequisite, ensure your bam files are located within position 29mb -34mb on chromosome 6. If not, you can extract the files using:

samtools index "path to sorted_bam"
samtools view -b "path to sorted_bam" "6:29000000-34000000" > "your output file"

Installation

Nextflow

wget -qO- https://get.nextflow.io | bash

HLA-LA
```
conda install -c bioconda hla-la
```

Reference graph

Download the data package (2.3G)

wget http://www.well.ox.ac.uk/downloads/PRG_MHC_GRCh38_withIMGT.tar.gz

Index the graph, can take a few hours and might take up to 40G of memory.
```
HLA-LA.pl --action prepareGraph --PRG_graph_dir PRG_MHC_GRCh38_withIMGT
```

Running the pipeline

The pipeline does not require installation as NextFlow will automatically fetch it from GitHub.

Test data

To execute the pipeline on test dataset run:

 nextflow run nanjalaruth/hla_typing_using_HLA-LA -profile test -r main --reference_genome "path to the graph reference genome <hg19>" -resume

Own data

Start running your own analysis either by using flags as shown below:

nextflow run nanjalaruth/hla_typing_using_HLA-LA -profile slurm -resume --input "*.bam" --reference_genome "path to the graph reference genome"

or run your own analysis by modifying the conf/test.config file to suit the path to your data location and then run the command as below:

 nextflow run nanjalaruth/hla_typing_using_HLA-LA -profile slurm -c <path to your edited config file> -resume

To run the updated version of this pipeline, run:

 nextflow pull nanjalaruth/hla_typing_using_HLA-LA

Arguments

Required Arguments

Argument	Usage	Description
-profile	\<base,slurm>	Configuration profile to use. Slurm is a job scheduler, you could otherwise use pbs
--input	\</project/*.bam>	Directory pattern for bam files.
--reference_genome	\<hg19>	Path to the reference genome to which the samples will be mapped

Support

I track open tasks using github's issues

nanjalaruth / hla_typing_using_HLA-LA

readme