Haplotyping workflow

Comparison of allelic variants and haplotype definitions

The haplotyping workflow module performs the following operations:

• Identification of allele variants shared with reference haplotypes.
• Prioritisation of haplotype matches.
• Identification of the highest scoring haplotype.

The pipeline outputs three files per barcode:

• A {barcode}.matches.json file which contains all of the match information per barcode
• A {barcode}.matches.txt file which contains a human readable summary of the per-allele matches
• A {barcode}.haplotype.txt file which contains the haplotype assignment per allele

Requirements

• Conda/Miniconda

Installation

• Clone the repository

  • git clone https://github.com/lumc-pgx/haplotyping.git

• Change to the haplotyping directory

  • cd haplotyping

• Create a conda environment for running the pipeline

  • conda env create -n haplotyping -f environment.yaml

• In order to use the pipeline on the cluster, update your .profile to use the drmaa library:

  • echo "export DRMAA_LIBRARY_PATH=libdrmaa.so.1.0" >> ~/.profile
  • source ~/.profile

Configuration

Pipeline configuration settings can be altered by editing config.yaml.

Execution

• Activate the conda environment
  • source activate haplotyping
• For parallel execution on the cluster
  • pipe-runner
• To specify that the pipeline should write output to a location other than the default:
  • pipe-runner --directory path/to/output/directory