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"
wget -qO- https://get.nextflow.io | bash
conda install -c bioconda hla-la
wget http://www.well.ox.ac.uk/downloads/PRG_MHC_GRCh38_withIMGT.tar.gz
HLA-LA.pl --action prepareGraph --PRG_graph_dir PRG_MHC_GRCh38_withIMGT
The pipeline does not require installation as NextFlow
will automatically fetch it from GitHub
.
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
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
nextflow pull nanjalaruth/hla_typing_using_HLA-LA
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 |
I track open tasks using github's issues